Robert Castelo
| Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/GSVA |
| git_branch: devel |
| git_last_commit: 6db4456 |
| git_last_commit_date: 2024-07-08 04:20:12 -0400 (Mon, 08 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 905/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GSVA 1.53.4 (landing page) Robert Castelo
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
|
To the developers/maintainers of the GSVA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GSVA.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: GSVA |
| Version: 1.53.4 |
| Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GSVA.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GSVA_1.53.4.tar.gz |
| StartedAt: 2024-07-16 00:40:39 -0400 (Tue, 16 Jul 2024) |
| EndedAt: 2024-07-16 00:49:34 -0400 (Tue, 16 Jul 2024) |
| EllapsedTime: 535.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GSVA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GSVA.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GSVA_1.53.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/GSVA.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GSVA/DESCRIPTION' ... OK
* this is package 'GSVA' version '1.53.4'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GSVA' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/GSVA/libs/x64/GSVA.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'runTests.R'
Running 'test_gsva_newapi.R'
Comparing 'test_gsva_newapi.Rout' to 'test_gsva_newapi.Rout.save' ...16,21c16,21
< Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
< as.data.frame, basename, cbind, colnames, dirname, do.call,
< duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
< lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
< pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
< union, unique, unsplit, which.max, which.min
---
> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
> Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
> table, tapply, union, unique, unsplit, which.max, which.min
38,45c38
< I, expand.grid, unname
<
<
< Attaching package: 'IRanges'
<
< The following object is masked from 'package:grDevices':
<
< windows
---
> expand.grid, I, unname
168c161
< KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.22920126 -0.264187722 -0.37401687 0.291350766 0.17081880 -0.45702585 0.5003620 -0.09626897 -0.47879766 0.2009603094 0.092846463 0.39386860 -0.10064875 0.25767347 -0.006960737 -0.323002689 0.54088138 0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429 0.206128783 -0.38394575 -0.26111852 0.11124358 -0.307607156 -0.23108674 0.118623744 0.40568230 -0.35928390 -0.2287986403 0.0674126870 -0.194909729 0.406279736
---
> KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.22920126 -0.264187722 -0.37401687 0.291350766 0.17081880 -0.45702585 0.5003620 -0.09626897 -0.47879477 0.2009603094 0.092846463 0.39386860 -0.10064875 0.25767347 -0.006960737 -0.323002689 0.54088138 0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429 0.206128783 -0.38394575 -0.26111852 0.11124358 -0.307607156 -0.23108674 0.118623744 0.40568230 -0.35928390 -0.2287986403 0.0674126870 -0.194909729 0.406279736
170c163
< KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.39571823 -0.352221233 -0.14016244 0.358512977 0.16414025 -0.26589439 0.6674822 0.17953342 -0.55050994 0.0562838685 0.021675321 0.57648156 0.11371008 0.29864451 0.104942610 -0.504014044 0.57693561 0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598 0.1109189257 0.023878095 -0.34214747 -0.25852067 0.28121726 -0.435798801 -0.31480707 -0.007553482 0.26670234 -0.45518879 -0.4532774636 0.2948129840 -0.267281290 0.463433745
---
> KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.39571823 -0.352221233 -0.14016244 0.358512977 0.16414025 -0.26589439 0.6674822 0.17953342 -0.55049088 0.0562838685 0.021675321 0.57648156 0.11371008 0.29864451 0.104942610 -0.504014044 0.57693561 0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598 0.1109189257 0.023878095 -0.34214747 -0.25852067 0.28121726 -0.435798801 -0.31480707 -0.007553482 0.26670234 -0.45518879 -0.4532774636 0.2948129840 -0.267281290 0.463433745
173c166
< KEGG_GALACTOSE_METABOLISM 0.06062020 -0.424855520 -0.03930301 0.349652791 -0.12188569 -0.46296074 0.5180153 -0.01789657 -0.35347309 0.2446797481 0.473003017 0.34499007 0.34112213 0.25024239 0.250381767 -0.453215048 0.57769569 0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855 0.056226416 -0.07839585 0.07879640 0.27290820 -0.414140702 -0.36050412 -0.191532611 0.39567826 -0.53298775 -0.4127888920 0.3440494486 -0.178365423 0.513262262
---
> KEGG_GALACTOSE_METABOLISM 0.06062020 -0.424855520 -0.03930301 0.349652791 -0.12188569 -0.46296074 0.5180153 -0.01789657 -0.35356594 0.2446797481 0.473003017 0.34499007 0.34112213 0.25024239 0.250381767 -0.453215048 0.57769569 0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855 0.056226416 -0.07839585 0.07879640 0.27290820 -0.414140702 -0.36050412 -0.191532611 0.39567826 -0.53298775 -0.4127888920 0.3440494486 -0.178365423 0.513262262
180c173
< KEGG_PURINE_METABOLISM 0.20191160 -0.108479208 -0.10596002 0.292297651 -0.05290036 -0.02776887 0.3629813 0.19221693 -0.19257010 -0.1570618328 0.049458419 0.10941378 -0.11575356 0.10624767 0.139611752 -0.104415107 0.24845743 0.18074380 0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986 0.14562604 -0.027395894 0.03493636 0.032161754 -0.01145234 0.00244119 -0.1717349277 0.1040248755 -0.158512548 -0.016876129
---
> KEGG_PURINE_METABOLISM 0.20191160 -0.108479208 -0.10596002 0.292297651 -0.05290036 -0.02776887 0.3629813 0.19221693 -0.19257184 -0.1570618328 0.049458419 0.10941378 -0.11575356 0.10624767 0.139611752 -0.104415107 0.24845743 0.18074380 0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986 0.14562604 -0.027395894 0.03493636 0.032161754 -0.01145234 0.00244119 -0.1717349277 0.1040248755 -0.158512548 -0.016876129
Running 'test_plage_newapi.R'
Comparing 'test_plage_newapi.Rout' to 'test_plage_newapi.Rout.save' ...16,21c16,21
< Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
< as.data.frame, basename, cbind, colnames, dirname, do.call,
< duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
< lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
< pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
< union, unique, unsplit, which.max, which.min
---
> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
> Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
> table, tapply, union, unique, unsplit, which.max, which.min
38,45c38
< I, expand.grid, unname
<
<
< Attaching package: 'IRanges'
<
< The following object is masked from 'package:grDevices':
<
< windows
---
> expand.grid, I, unname
Running 'test_ssgsea_newapi.R'
Comparing 'test_ssgsea_newapi.Rout' to 'test_ssgsea_newapi.Rout.save' ...16,21c16,21
< Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
< as.data.frame, basename, cbind, colnames, dirname, do.call,
< duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
< lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
< pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
< union, unique, unsplit, which.max, which.min
---
> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
> Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
> table, tapply, union, unique, unsplit, which.max, which.min
38,45c38
< I, expand.grid, unname
<
<
< Attaching package: 'IRanges'
<
< The following object is masked from 'package:grDevices':
<
< windows
---
> expand.grid, I, unname
85a79,81
> [1] "Calculating ranks..."
> [1] "Calculating absolute values from ranks..."
> [1] "Normalizing..."
133a130,132
> [1] "Calculating ranks..."
> [1] "Calculating absolute values from ranks..."
> [1] "Normalizing..."
164a164,166
> [1] "Calculating ranks..."
> [1] "Calculating absolute values from ranks..."
> [1] "Normalizing..."
194a197,199
> [1] "Calculating ranks..."
> [1] "Calculating absolute values from ranks..."
> [1] "Normalizing..."
222a228,230
> [1] "Calculating ranks..."
> [1] "Calculating absolute values from ranks..."
> [1] "Normalizing..."
Running 'test_zscore_newapi.R'
Comparing 'test_zscore_newapi.Rout' to 'test_zscore_newapi.Rout.save' ...16,21c16,21
< Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
< as.data.frame, basename, cbind, colnames, dirname, do.call,
< duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
< lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
< pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
< union, unique, unsplit, which.max, which.min
---
> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
> Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
> table, tapply, union, unique, unsplit, which.max, which.min
38,45c38
< I, expand.grid, unname
<
<
< Attaching package: 'IRanges'
<
< The following object is masked from 'package:grDevices':
<
< windows
---
> expand.grid, I, unname
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.20-bioc/meat/GSVA.Rcheck/00check.log'
for details.
GSVA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GSVA ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'GSVA' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kernel_estimation.c -o kernel_estimation.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ks_test.c -o ks_test.o gcc -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c register_cmethods.c -o register_cmethods.o gcc -shared -s -static-libgcc -o GSVA.dll tmp.def kernel_estimation.o ks_test.o register_cmethods.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-GSVA/00new/GSVA/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GSVA)
GSVA.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> oldWarnOptionValue <- options(warn=1)
> BiocGenerics:::testPackage("GSVA")
Timing stopped at: 0 0 0
Error in DEACTIVATED("HDF5Array is not yet supported by the new API.") :
HDF5Array is not yet supported by the new API.
Running unit tests for input data containers.
Running unit tests for the new API.
Running unit tests for gsvaParam.
Running unit tests for plageParam.
Running unit tests for ssgseaParam.
Running unit tests for zscoreParam.
Running unit tests for sparse methods.
Please bear in mind that this method first scales the values of the gene expression data. In order to take advantage of the sparse Matrix type, the scaling will only be applied to the non-zero values of the data. This is a provisional solution in order to give support to the dgCMatrix format.
Please bear in mind that this method first scales the values of the gene expression data. In order to take advantage of the sparse Matrix type, the scaling will only be applied to the non-zero values of the data. This is a provisional solution in order to give support to the dgCMatrix format.
Running unit tests for ssGSEA.
RUNIT TEST PROTOCOL -- Tue Jul 16 00:44:57 2024
***********************************************
Number of test functions: 8
Number of deactivated test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
GSVA RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8
Number of deactivated test functions: 1
Number of errors: 0
Number of failures: 0
> options(warn=oldWarnOptionValue[["warn"]])
>
> proc.time()
user system elapsed
12.56 1.12 13.18
GSVA.Rcheck/tests/test_gsva_newapi.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> ## 2023-11-10 axel: simple test script for method GSVA, new API
>
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db
> library(GSVA)
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 1.4171739 -1.3444519 -0.99052898 0.4203395 1.30716224
g2 -0.7281951 0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754 0.09779699 -0.6792548 -0.09124045
g4 1.0735382 1.3156255 0.15588330 -1.8079608 0.48531108
g5 0.7229884 -0.9162342 1.93982245 0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> gsvaPar <- gsvaParam(X, gs)
> gsva.es <- gsva(gsvaPar, verbose=FALSE)
> dim(gsva.es)
[1] 100 30
> gsva.es[seq.int(min(nRowsToPrint, nrow(gsva.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 -0.108156444 0.16592613 -0.143808928 0.11391879 -0.08600850 -0.1734242744 0.178707342 0.017723667 0.094198786 0.103231011 0.098990086 0.056687452 -0.19582109 0.012296862 0.162223446 -0.114766326 -0.293330673 0.126367035 0.228829622 -0.14884956 0.026620947 -0.301784054 -0.30631599 0.235331985 0.04638816 -0.1100099596 -0.0999704513 -0.046424755 0.293447378 -0.17344608
gs2 -0.078540545 0.19300391 0.079182716 0.07049058 0.04007773 0.1715072044 0.203277577 -0.081465590 0.233451158 -0.280324459 0.037382517 0.025061259 0.10845168 -0.059159170 0.026844586 -0.179610527 -0.014413382 -0.006820970 0.160768137 -0.03932893 -0.108749046 -0.282019527 0.08605189 0.088382420 0.06394081 0.0207049280 0.2183498851 0.084518747 -0.272555793 -0.17000646
gs3 -0.012507633 -0.25351738 0.102368361 0.03512929 -0.04994980 0.2133058738 0.039178136 0.191682501 -0.398094428 0.343111543 -0.076791958 0.119069468 0.20772960 -0.421116272 0.459538877 -0.026465562 0.049041138 0.038384015 -0.227781747 -0.09134458 -0.514150386 0.102494298 -0.20024782 0.058491931 0.31836609 0.0290482835 -0.1935787866 0.254416177 -0.017322981 0.13715416
gs4 -0.083248846 0.02946102 -0.042556750 0.08145113 -0.05401867 0.1055847509 -0.158661388 0.009278808 -0.107756958 -0.016141791 -0.033233344 0.016122676 -0.08342913 -0.003621483 0.141048462 -0.001454018 0.129386313 -0.062100704 -0.110927318 -0.16530100 -0.059697155 0.032076675 0.03158162 0.038234047 -0.03942766 0.0886365597 -0.0782910850 0.014516781 -0.046885905 0.20075530
gs5 0.129917233 -0.14323749 -0.172890947 0.13411529 0.09628743 0.0265475253 0.050870369 0.174122516 0.081836827 -0.011085820 0.023089550 0.056006287 -0.07140253 0.055193034 -0.091548680 -0.149492965 0.037312222 0.002985924 -0.144101863 -0.01888358 -0.065961297 -0.132468115 -0.06377434 0.028402402 -0.07610908 0.0853809151 0.0806035221 -0.015568714 -0.047153650 0.01778386
gs6 -0.284972014 0.13823428 -0.210772112 -0.05757943 0.10388699 0.1439391564 0.109157571 0.077447106 0.001144118 0.181326976 -0.019716350 -0.006386486 -0.06006467 -0.189315716 0.005405993 -0.001953525 0.006055122 0.159361735 -0.089341440 0.02743543 0.000728224 -0.178928406 0.19578172 -0.036394549 -0.07703071 0.0784321711 -0.0863070990 -0.033617568 -0.088131880 0.09008523
gs7 0.028701964 0.23235456 0.119915418 -0.01970966 -0.13698294 0.0031401764 -0.218020511 -0.195273449 0.038952752 -0.232984107 0.037413398 0.092363954 0.18259907 0.053162383 0.097674825 -0.128073348 0.073567722 0.115641271 0.030537867 -0.13049139 -0.057022525 0.056026838 0.06828574 -0.001000666 -0.06071745 0.0039744122 -0.0005585096 -0.009440488 0.080790372 -0.09940113
gs8 0.006333045 0.01460128 0.136198133 -0.07889863 -0.11123825 0.0387444491 -0.002037746 0.040187847 -0.121686486 -0.095484760 0.052264970 0.150236692 0.04926308 -0.109888308 0.100412242 0.146400621 -0.156050604 0.018922498 0.067657595 -0.05343596 -0.068927042 -0.080941576 0.07501949 0.007660285 0.16079137 -0.2682601362 0.1012140737 0.042776107 0.002111495 -0.05482992
gs9 -0.175865699 -0.19690763 0.060751759 0.18933359 -0.25345038 -0.5016097134 -0.138854281 -0.543295516 -0.263543869 0.275493131 0.127068488 -0.189846149 -0.25784051 -0.094258279 0.079039460 -0.165487585 0.343543465 0.357424759 0.292115383 -0.02178526 0.058171774 -0.034552813 0.23880691 0.043569142 -0.02980941 0.2945856247 -0.0219706361 -0.176772536 0.532204432 0.15142975
gs10 0.098112170 -0.35611542 -0.056579211 -0.21958226 0.08809195 0.0009137342 0.405507850 -0.115481827 -0.187608357 0.275280555 -0.119567715 0.109071314 -0.25466878 0.000375529 0.367963754 0.188641874 -0.079209335 0.256239935 -0.125622141 -0.11854834 0.255106701 0.471876454 -0.37385722 0.223837887 0.02289076 -0.4287911223 0.0067681070 -0.240476346 0.088671730 -0.17764056
gs11 0.098198198 0.25911849 -0.038035464 -0.21771367 0.50403680 0.4428564710 0.303629955 0.175137764 0.098749107 0.336354436 0.130586418 -0.052651015 -0.20599477 -0.223219535 -0.250927738 -0.509205728 -0.444857809 -0.045479124 0.088547534 -0.02722749 -0.099107700 -0.092392768 0.05594057 -0.069222681 -0.02071750 -0.5973180441 -0.1580304020 0.577149382 0.298070860 -0.07458713
gs12 0.096490065 -0.02605933 -0.022030360 -0.13719093 0.02682772 0.0434813048 -0.028867424 0.014475285 0.133723333 0.034558185 0.137695531 -0.258037193 -0.02835015 -0.064346101 -0.026710216 -0.269826308 0.021532017 -0.047943462 -0.022440279 0.16687604 0.055835937 0.023685654 -0.06486901 -0.020025683 0.02178566 0.0480895384 0.1113867112 0.059878337 -0.055779061 0.06729589
gs13 0.223982459 0.20679601 0.258716670 -0.20136940 -0.20071529 0.2464442479 0.258963232 -0.110149641 -0.089442650 0.205739275 -0.165291846 -0.150888458 -0.15226578 -0.404364664 -0.005312768 -0.100572023 -0.220803462 -0.043370760 0.309185329 -0.08715961 0.326811093 0.080713114 -0.10705436 0.116977351 0.19046277 -0.1469583728 0.1367810954 -0.242162288 -0.021163531 -0.29632096
gs14 0.024001674 -0.26723135 -0.398236422 0.24294428 0.04991522 -0.1433770344 0.399168882 -0.248011836 -0.121856855 -0.141859978 -0.080548602 0.105372091 0.28663719 0.303516623 0.320574969 -0.044182057 -0.177554197 -0.058580934 0.063071784 0.11623764 0.096538164 -0.055513833 -0.42073250 0.001550673 0.16488985 0.0464015474 -0.0156188987 -0.085775207 -0.160086709 0.12477191
gs15 0.107236756 0.02674424 0.186569862 -0.12214378 -0.06518532 -0.0612943018 -0.111903203 0.049803938 0.044035633 -0.049752082 -0.024069020 0.205529366 -0.10569735 0.002119758 -0.140742436 0.185481189 -0.005853900 -0.101479169 -0.001425559 0.08308067 0.020882554 0.051697561 0.05197634 0.276490515 0.09494653 -0.1604533503 -0.1106884939 -0.115292890 -0.212477678 -0.04261664
gs16 -0.189661090 0.18212481 -0.194291062 0.11967900 -0.10434220 -0.1191397416 0.039057392 -0.039343595 -0.060222683 -0.067506938 -0.160259179 0.001722109 0.14378774 -0.013559159 0.165627072 -0.022929924 -0.032725397 -0.021268004 -0.036164578 0.04105859 0.054069320 -0.023626997 0.01312951 -0.066479935 0.03594310 0.0510113983 0.0168947880 -0.006306806 0.182001699 0.08182702
gs17 -0.224154710 -0.06839924 0.011942989 0.06596303 -0.01898285 -0.0787236017 0.262432764 0.128350415 0.107171841 -0.036418415 0.004430908 -0.152391953 0.13910575 -0.034949755 0.129033846 -0.096575805 0.027781998 0.086966986 -0.057041784 0.06413185 -0.088718911 0.119981085 0.07640730 -0.116205119 -0.19211361 0.0949234199 -0.0301489984 0.007364308 -0.021454055 -0.05405507
gs18 0.144462699 0.15190319 -0.005644637 0.13442504 -0.06851005 -0.0650767309 0.132965207 -0.072143414 0.065609258 -0.169604968 0.149226527 -0.127080390 0.15127334 0.001524110 -0.096672404 0.138052662 0.156721335 -0.113260460 -0.055010361 -0.11281271 -0.081498926 -0.062627336 0.01138976 0.083051492 -0.11650835 -0.0644334115 0.0158668194 -0.035534584 -0.216520795 0.25451909
gs19 -0.114727405 0.11606640 0.014639537 -0.04539144 -0.15632885 -0.3008348682 -0.045227873 0.057911106 0.077993588 0.122127072 0.004180167 -0.010181304 -0.13058749 -0.017522472 -0.063018173 0.096067773 0.059813582 -0.042255247 -0.110140982 0.28341206 -0.057751403 -0.062970017 -0.26428505 -0.087882907 -0.06031966 0.2005231419 0.0555096129 -0.119697294 0.158883568 0.13631818
gs20 -0.250434807 -0.04667705 0.049213711 0.05304980 0.15123353 0.1091531262 0.061807069 -0.184158384 0.116516282 -0.024996495 0.050439116 0.062684587 -0.03915131 -0.056457080 -0.298840942 0.163262104 -0.029174994 0.169067340 0.055693074 0.03338657 0.068733916 0.047318574 0.05085801 0.007052938 -0.13510237 -0.0802436967 -0.0251620082 -0.048587104 -0.071021904 -0.04269538
gs21 0.135378868 0.16802591 -0.029364914 -0.05595578 0.06148837 0.0971278669 0.093694989 -0.069804459 0.025767351 -0.016170741 -0.101534883 -0.120160395 0.04062725 0.048721679 0.095192931 -0.186471874 -0.048112890 -0.212895052 -0.006971640 -0.06755367 -0.127602218 -0.002382844 -0.01605748 -0.001335954 -0.11991648 0.2219113569 0.1352495887 0.023381243 0.045687474 0.09964681
gs22 -0.163680317 0.18690317 -0.148456673 -0.05079516 0.24365056 -0.0822628950 0.098769260 -0.142649660 -0.444454723 0.065727715 0.247342235 -0.167215276 0.14197399 0.112681184 -0.092957822 -0.152497158 -0.190680030 0.035186284 -0.035122161 0.07290296 0.002562072 0.032535170 0.26649228 0.318514935 -0.22440917 -0.0178361034 -0.3138866671 0.416817320 -0.314242601 -0.02772554
gs23 0.018766631 0.11521514 -0.014809625 0.06153311 0.12707575 0.1281180662 -0.064456890 -0.030536563 -0.129612935 -0.015034995 0.129955588 0.057111134 -0.22165829 0.160845001 0.108799691 0.090243195 0.008299278 0.041996865 0.155112600 -0.08959788 0.079998925 0.013571384 -0.27985106 -0.134362071 0.05587958 0.0900157601 -0.0306708210 -0.124824057 -0.125258066 0.03409850
gs24 0.389869244 0.28790219 -0.049088266 -0.14811747 -0.19067680 -0.3358219719 -0.236811755 0.135616593 -0.238985451 0.206904619 0.248194834 -0.112405472 0.09072771 -0.142415602 -0.383217061 0.363554498 0.187395921 -0.327457108 -0.592050113 0.15802933 0.479729800 -0.150610477 0.28243874 -0.202986917 0.12126635 0.0007700638 -0.0280707676 0.049077412 -0.212219932 0.12363971
gs25 0.093907002 -0.08177613 0.137542184 0.01817976 -0.07335024 -0.2779884851 -0.010150488 -0.109990320 -0.023037802 -0.006390004 0.088013029 -0.003651291 -0.16541049 0.090206786 -0.091065047 0.089689390 0.061729248 0.223324387 0.050045901 -0.08299866 0.221155832 -0.246784249 0.32074709 0.037550027 -0.16709326 -0.1213934826 0.1061837744 0.016007278 0.065201658 -0.19524119
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+ grep("^REACTOME", names(c2BroadSets)),
+ grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- gsvaParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+ minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS -0.14418012 -3.133817e-01 -0.391171673 0.21340339 0.398980386 -0.03179434 0.17524757 0.26705934 0.196519789 0.07076882 0.0145998761 0.27413667 0.083361420 -0.10575923 -0.189608055 -0.30624818 -0.25363521 -0.371666584 0.131382543 0.122449569 0.19101441 -0.452577261 -0.23105310 0.10274129 0.13624827 -0.007124138 0.15976388 -0.102152201 -0.19832123 0.202573385 0.378578854 0.288352608 0.0016120367 -0.36268281 0.110141001 0.255205365
KEGG_CITRATE_CYCLE_TCA_CYCLE -0.20263269 2.546732e-01 0.012685194 -0.23423639 0.166963123 -0.19060735 -0.09504444 0.02350579 0.252153864 -0.29870033 0.3426900775 0.11865360 0.158070942 0.43950013 -0.113554675 -0.41027161 -0.51496205 0.101464045 0.023147027 0.213518494 -0.29129288 -0.365361233 0.19537441 0.34046332 -0.29053602 -0.136804277 -0.03945536 -0.046177552 -0.15861718 -0.197363503 0.005305269 0.139063426 0.3753961988 -0.11672606 0.399275124 0.081808177
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.13384996 -3.426199e-01 0.011055653 0.10473591 0.533196442 0.08319882 -0.07286230 0.33986046 0.183712674 -0.02112598 0.3436817431 0.14970027 0.045619795 0.34106103 -0.319187004 -0.12337277 -0.52047602 -0.079296210 0.246091695 0.007442165 0.29667112 -0.493628865 -0.37567090 0.04398852 -0.10380781 -0.066433829 0.07248245 -0.134640505 -0.28388477 -0.007933863 -0.010660832 0.409249866 -0.0593083889 -0.20730184 0.135344012 0.328985231
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS -0.04814412 2.649390e-01 -0.247781616 -0.57051071 -0.151893395 -0.12257602 -0.22484133 0.15415444 0.170044654 -0.41770107 0.4059486427 0.32600904 -0.337637004 0.45224654 0.240860923 -0.52860069 0.06878373 0.238734193 0.199127444 0.197382585 0.19194776 -0.280713555 -0.14573199 -0.07489534 -0.17115751 -0.356340540 0.19199016 0.464332824 -0.30954147 0.066784875 0.107764195 -0.244087607 -0.0038072528 -0.15577831 0.159465388 0.173314410
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM -0.05277464 -2.559473e-01 -0.272606595 0.02654463 0.466256330 -0.07516578 -0.08827428 0.17940166 0.175438074 0.08335115 0.1949276528 0.03263319 -0.037187373 0.21769233 -0.056026638 -0.21875825 -0.41789351 -0.167172773 -0.116119580 0.028778964 0.18475990 -0.006106045 -0.35983263 0.04835565 0.13058334 0.320582420 0.14792337 -0.356458053 -0.32573808 -0.200330955 0.256816456 0.243425591 0.1799096212 0.04042810 0.078246331 0.111827102
KEGG_GALACTOSE_METABOLISM -0.51060398 -3.263793e-01 -0.339445527 0.18058711 0.590147665 -0.05433206 -0.02631533 0.01150479 0.112418121 0.20086931 0.0758757516 0.18135031 0.172899748 0.09960453 -0.419887121 -0.30998273 -0.41031657 -0.552555465 0.134889700 0.312990925 0.40442648 -0.314101297 -0.45866474 0.24674708 0.36744079 -0.300764693 0.46807677 -0.119986976 -0.47812839 -0.137744193 0.179487063 0.362685887 -0.1178698280 -0.27717714 0.333123866 0.570589012
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.39533716 1.058190e-01 -0.055948980 0.32042238 0.117469296 -0.47857258 -0.27397801 0.48975038 -0.092440191 -0.05795173 -0.0744286061 -0.21729660 0.193086799 0.31390769 0.038143586 0.04976352 0.06941386 -0.243260211 -0.075892533 -0.136936205 -0.70456483 -0.248431863 0.04441643 0.16407617 0.10523266 0.201548537 -0.63041976 -0.064796304 -0.42586995 0.071454531 0.327254119 -0.007811551 0.2006101479 0.02592733 -0.340917460 0.307433176
KEGG_FATTY_ACID_METABOLISM 0.03299573 1.864144e-01 0.209909423 -0.24436698 0.207945636 -0.12244431 -0.23816823 0.49912101 0.388462885 -0.20945911 0.0991996326 0.28644900 0.027816218 0.13251193 -0.076840810 -0.35401475 -0.26281629 0.022061212 0.092216454 0.131207009 -0.32302048 -0.043107375 -0.17671170 0.13894499 -0.29064351 -0.119433589 -0.42265454 -0.103764267 -0.09629923 -0.114672086 0.246246155 0.137119878 0.4886075270 -0.07587824 0.017144468 0.033774833
KEGG_STEROID_BIOSYNTHESIS 0.19815359 -1.774636e-01 -0.495105675 -0.25914877 0.190294265 -0.32446562 0.40274807 0.55575502 0.334577780 -0.30738356 0.0995344990 0.02714295 -0.341505856 0.33481474 0.483575947 -0.46782536 -0.41070981 0.363247663 -0.316476327 0.186672062 0.06775463 -0.460614122 -0.03811347 0.10403630 0.19161113 -0.276517655 -0.31751788 -0.335291201 0.04610323 0.498441393 0.203641470 0.258537460 0.1025848927 0.32986280 0.106728771 0.044375942
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS -0.22772338 3.313823e-01 -0.045122587 0.34604215 -0.326387527 -0.37238068 0.38109784 0.50612839 -0.279733901 -0.46710624 -0.3566433892 0.38150788 -0.160181485 0.32343792 -0.389633800 -0.04093348 -0.34781666 0.439898619 -0.553153746 0.333311581 -0.41569720 0.089984351 0.11640121 0.49616048 -0.18515617 -0.288891006 -0.25307258 0.488505183 0.48932043 0.685621131 0.405112800 -0.410676806 0.0705999647 0.46798357 -0.050407919 -0.059580749
KEGG_STEROID_HORMONE_BIOSYNTHESIS 0.36585090 -4.158145e-02 -0.314872488 0.36177011 -0.117186424 -0.57565233 0.06555161 0.12421684 -0.154537531 -0.03651661 0.2548932547 -0.25983105 -0.191491808 -0.01727654 0.007925232 0.20173611 0.07385251 -0.151691776 -0.174246389 0.170112989 -0.31138189 -0.287770962 -0.32224067 0.25539717 0.10328113 -0.240352841 -0.02844086 0.115892938 0.20532852 0.092026010 0.444749927 0.138675375 -0.1017217201 0.19796954 -0.321674802 0.386149959
KEGG_OXIDATIVE_PHOSPHORYLATION -0.44614351 4.066706e-01 0.315683836 -0.38414333 -0.062919018 0.19858654 -0.22582769 0.04161922 -0.079644512 -0.05102341 0.3664592628 -0.09619084 0.197886790 0.31353680 -0.184933831 -0.36350759 -0.30233809 0.313796606 0.236200087 -0.322015323 -0.29790565 -0.196993574 -0.08707882 0.26462100 -0.24626717 0.241984062 0.12731683 -0.209160519 -0.13913537 -0.164019798 0.003657569 0.174518566 0.2846868562 -0.03739754 0.351418754 -0.151465743
KEGG_PURINE_METABOLISM -0.12658061 6.074446e-05 0.109942629 0.02507931 0.152633778 0.20438698 0.05049747 0.08805693 -0.163334045 -0.09018816 0.2671088095 0.13157027 0.002135794 0.19941825 -0.014318164 -0.19467600 -0.19570945 0.160038352 -0.003976608 -0.159354533 0.04953516 -0.237144513 -0.19729598 0.06518253 -0.20013531 0.065168510 -0.02813078 0.001056042 -0.03466977 -0.006764599 0.054072961 -0.010634495 0.1220901659 -0.14216130 0.002592869 -0.079175937
KEGG_PYRIMIDINE_METABOLISM -0.08169375 2.124920e-02 0.237112503 0.02740654 -0.007840300 0.24898451 -0.04095103 0.23335111 -0.156235016 -0.16193850 0.2906078400 0.19091514 -0.095748971 0.19881417 0.039922114 -0.17823010 -0.14678724 0.256232748 0.020947130 -0.088582706 0.16161796 -0.307232427 -0.08240158 0.03008501 -0.30460678 0.090542640 -0.09034804 -0.174657514 -0.09426947 -0.129635921 -0.040660453 -0.066351934 0.3336055751 -0.05856322 -0.032156131 -0.179871004
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM -0.13254287 -6.225182e-02 -0.134319540 -0.15729012 0.026834849 -0.22343907 0.14168564 0.30713913 -0.125172326 -0.17862058 -0.1731094263 0.30055821 -0.085420317 0.09882301 0.193697084 0.31425985 -0.31600195 -0.125372528 0.295397875 0.180199556 -0.20500280 0.058617241 -0.14777995 0.05091438 0.12367397 -0.040310943 -0.08013473 0.182346297 -0.10198293 0.197362551 0.285434513 0.083269169 -0.3708006909 -0.06111266 -0.243366412 0.222746237
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.10719371 -4.606961e-01 -0.180567057 0.09540174 0.245012608 -0.15656927 0.22420420 0.05451998 0.279637623 0.13353399 0.0588075025 -0.29202943 -0.043946876 0.01212064 0.153895823 0.41802493 -0.13778592 -0.372235469 -0.406109789 0.283133835 0.19519783 -0.020078578 -0.26407215 0.12285472 0.26704639 0.059250879 0.04897781 -0.250007490 -0.05255973 0.087369877 0.196707759 0.202125900 -0.4079062250 -0.14271079 0.201471466 0.148775715
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.31199860 -1.470030e-01 0.003351767 0.19314634 -0.069733318 0.03818098 0.14330053 0.29773728 0.199561609 -0.18575435 0.2414974155 0.26605667 -0.291208656 0.16923947 0.350632975 0.15181300 -0.22743772 -0.019995533 0.165918443 -0.282999158 0.23210130 -0.390498560 0.09366624 -0.22502795 -0.10851096 -0.372625112 -0.43938185 0.172251073 0.03236597 0.169871903 -0.116676657 -0.006200565 -0.2279015972 -0.18233790 0.215082562 -0.127529151
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.13690035 3.114732e-01 0.066312869 -0.42482813 -0.090282754 0.17692622 -0.19729696 0.34694241 0.407012719 -0.49732087 0.4128185814 0.21841977 0.209032500 0.22079194 0.098804076 -0.28545919 -0.23815839 -0.180999045 0.227212036 0.266627679 -0.26343085 -0.365422361 -0.24682867 0.09025547 -0.26797947 -0.355998344 -0.48059599 0.287997010 0.04787260 0.218397773 0.054137782 -0.098018435 0.3267593437 -0.45818263 0.271972064 0.296388858
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.21018404 3.311632e-01 -0.305891231 -0.40884425 0.154601400 0.29113672 -0.24105148 -0.24181442 0.181954325 -0.58092775 0.4049453421 0.24614645 0.133009367 0.50265059 0.272676320 0.03717033 -0.02236702 -0.145501442 0.138011286 0.443984308 0.39650468 -0.290692301 -0.12632929 -0.19057616 -0.07228556 -0.257796347 0.05090257 -0.239289854 -0.27079693 -0.411150458 0.112237525 -0.264314957 -0.4438365768 0.26411102 0.709862664 -0.016572984
KEGG_LYSINE_DEGRADATION -0.05052662 1.114498e-02 0.229382702 0.09046133 0.038741982 0.28814839 -0.18110222 0.18668860 0.200429660 -0.15730855 0.2122002799 0.15678305 0.291243079 -0.09136060 0.075543036 -0.20498916 -0.11109630 -0.119030450 -0.042852292 0.236306523 0.07759842 -0.290175631 -0.01746742 -0.21890493 -0.20792480 0.077495323 -0.27615714 0.039431840 -0.12276895 -0.053898732 -0.080541817 -0.016639943 0.0009973473 -0.40134082 0.137262457 0.007682097
KEGG_ARGININE_AND_PROLINE_METABOLISM -0.22800596 4.906206e-02 -0.042335265 0.01804139 0.185198410 -0.31622084 0.33887630 0.14716659 -0.125964421 -0.04372424 -0.1317531626 -0.23684263 -0.084937438 0.12230128 0.041463950 0.01888723 -0.23867163 -0.418034734 0.100108084 -0.024241225 0.06662724 0.062701077 -0.18005295 0.28126338 0.26487393 0.117918976 0.03282485 -0.267823209 -0.11043893 0.310700224 0.208244241 0.293517379 -0.1408712737 0.08681285 0.022305834 0.089895339
KEGG_HISTIDINE_METABOLISM 0.36390137 2.365551e-01 -0.116603139 -0.05003836 0.327736448 -0.21045969 -0.09444006 0.07411204 0.004241093 -0.21347825 -0.2759296517 -0.09004815 -0.220892221 -0.04865282 0.223799615 0.07800378 0.10695352 0.008719129 -0.157708191 -0.206105926 -0.07079359 0.329843813 -0.03292310 -0.12534816 0.15073847 -0.369373567 -0.44170643 0.302626017 -0.35207965 0.319661614 0.084963193 -0.328337412 0.0562137944 -0.01801214 -0.140975452 -0.224081075
KEGG_TYROSINE_METABOLISM 0.20007757 1.721769e-01 -0.037643348 -0.19625928 -0.075882501 -0.12591313 0.33248542 -0.07760137 -0.191628836 -0.18678014 0.0004931861 -0.41470470 -0.197618861 0.44585904 0.460970463 -0.23734373 0.06323644 0.447147523 -0.339999748 -0.263094997 0.32393110 0.148291697 -0.02476993 -0.16845439 -0.05628810 -0.228433500 -0.09241908 0.205241359 -0.14005676 -0.123163041 0.280135889 -0.404510468 -0.0076082103 0.41987347 0.046111365 -0.109788331
KEGG_PHENYLALANINE_METABOLISM 0.14876060 3.091885e-01 -0.425309307 0.03290077 0.007314721 -0.44139027 0.41683218 0.00264260 -0.665142859 0.33683691 -0.1354678721 -0.56429899 -0.339302707 0.23461582 0.388641234 -0.14178018 -0.13963600 0.402700359 -0.060552296 0.198533242 0.30608114 -0.367173008 0.39977893 0.09861950 0.19457836 -0.450408082 0.02414787 0.419408775 0.14007478 -0.167643347 0.038509810 -0.118899152 -0.4538199574 0.58568820 0.155660090 -0.409252364
KEGG_TRYPTOPHAN_METABOLISM 0.02771378 7.276144e-02 0.164993365 -0.04842795 0.275480475 -0.39691784 -0.07428901 0.25507776 0.187930224 -0.16961352 -0.0772668699 0.10285172 -0.067196121 0.10898541 -0.204308026 -0.07494849 -0.14783141 -0.200577850 0.338704351 0.030157577 -0.38063449 -0.187786425 0.04954516 -0.07650680 0.08969431 -0.024503220 -0.28162674 0.105474846 -0.15358250 -0.063342825 0.059069680 -0.027357901 0.4168932938 0.08101763 -0.197098915 0.014085911
> pickrellPar <- gsvaParam(pickrellCountsArgonneCQNcommon_eset,
+ canonicalC2BroadSets, minSize=5, maxSize=500,
+ kcdf="Poisson")
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esrnaseq)[seq.int(min(nRowsToPrint, nrow(esrnaseq))),]
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.22920126 -0.264187722 -0.37401687 0.291350766 0.17081880 -0.45702585 0.5003620 -0.09626897 -0.47879766 0.2009603094 0.092846463 0.39386860 -0.10064875 0.25767347 -0.006960737 -0.323002689 0.54088138 0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429 0.206128783 -0.38394575 -0.26111852 0.11124358 -0.307607156 -0.23108674 0.118623744 0.40568230 -0.35928390 -0.2287986403 0.0674126870 -0.194909729 0.406279736
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.19534471 -0.202157014 -0.31886736 0.257353003 0.09452472 -0.14337654 0.5803541 0.21971004 -0.48460389 -0.0910376333 0.143073239 -0.01343428 0.21924711 0.14911562 0.331156020 -0.623445470 0.26517213 0.10217269 -0.244826732 -0.08275136 -0.13342326 -0.18991201 0.2222643203 -0.008264954 -0.27726336 -0.32626055 0.55391119 -0.274223459 -0.41600613 -0.239476881 0.23644605 -0.33329094 -0.4140553740 0.3505474463 -0.034676768 -0.002314262
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.39571823 -0.352221233 -0.14016244 0.358512977 0.16414025 -0.26589439 0.6674822 0.17953342 -0.55050994 0.0562838685 0.021675321 0.57648156 0.11371008 0.29864451 0.104942610 -0.504014044 0.57693561 0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598 0.1109189257 0.023878095 -0.34214747 -0.25852067 0.28121726 -0.435798801 -0.31480707 -0.007553482 0.26670234 -0.45518879 -0.4532774636 0.2948129840 -0.267281290 0.463433745
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.30431379 -0.234295884 -0.27059673 -0.245346011 -0.06027442 0.04706860 0.3884300 -0.15945758 0.02075130 -0.0008356316 0.156613047 -0.06726357 -0.25892817 0.47051857 0.358948273 -0.512413738 0.41386623 0.25956799 0.146563139 -0.10384415 0.29375249 -0.32605966 -0.3406774353 -0.079363956 -0.25850079 -0.55407022 0.33385389 0.468934430 -0.03022371 0.104853773 0.29678304 -0.14204144 0.3091341703 -0.0449204187 -0.269151573 0.118249851
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.11231761 -0.062748045 -0.04494400 0.443120939 -0.43879510 -0.26298245 0.4742617 0.10248633 -0.35537405 0.1685276920 0.144103617 0.21438430 0.15584943 0.01726953 0.220675430 -0.319381715 0.48892920 0.46105569 -0.426727337 -0.19856115 -0.31952483 0.01320194 -0.0382402740 -0.043511121 -0.35219578 -0.12906627 0.26969235 -0.290367845 -0.32181822 -0.242589300 0.35793456 -0.18587339 -0.3767879009 0.3985766414 -0.191002663 0.343416703
KEGG_GALACTOSE_METABOLISM 0.06062020 -0.424855520 -0.03930301 0.349652791 -0.12188569 -0.46296074 0.5180153 -0.01789657 -0.35347309 0.2446797481 0.473003017 0.34499007 0.34112213 0.25024239 0.250381767 -0.453215048 0.57769569 0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855 0.056226416 -0.07839585 0.07879640 0.27290820 -0.414140702 -0.36050412 -0.191532611 0.39567826 -0.53298775 -0.4127888920 0.3440494486 -0.178365423 0.513262262
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.51820705 0.039968658 -0.12377878 -0.036122904 0.31985771 -0.46527398 0.3988617 0.01038232 0.37687330 0.5270758669 -0.001642410 -0.11679805 -0.05628187 0.71772103 0.241534280 -0.289882381 0.69553991 0.45968207 0.296411226 -0.50738472 -0.41554732 -0.27269571 -0.0503383811 0.414487589 -0.23400690 -0.52790283 -0.51602401 0.445718811 -0.42330633 0.174908837 -0.07311759 0.34397307 0.2085765041 -0.3221300091 -0.392502279 0.284751348
KEGG_FATTY_ACID_METABOLISM 0.20886138 -0.242876900 -0.30320811 0.187550569 0.29327773 -0.08700294 0.5230685 0.27380231 -0.34116554 0.1472345229 0.062594388 0.08687790 0.14291551 0.51283780 0.291434806 -0.504476008 0.43294161 0.28219716 -0.304791635 -0.30535668 -0.18442492 -0.13244662 0.0150691534 0.283488006 -0.48289609 -0.49976986 0.09652311 -0.011347711 -0.31278105 0.239631877 0.20679322 -0.03829960 -0.3295649579 -0.0001742616 -0.141024787 0.339491609
KEGG_STEROID_BIOSYNTHESIS 0.33604553 0.078851347 -0.52590310 -0.263728541 0.32226372 0.07485904 0.3016156 0.28921483 -0.28561530 -0.6241643849 -0.150031690 -0.31567564 0.10600143 0.12621865 0.040239055 -0.372783352 -0.17192551 -0.02763554 -0.362917924 -0.33311374 -0.30449600 -0.19719698 0.6253409182 -0.008988029 0.19293398 0.09900056 0.13681999 -0.119518167 -0.26419274 -0.013995204 0.20395478 0.11325134 0.1626070916 0.5348477961 0.511074525 -0.190211341
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 0.15739882 0.084600205 -0.52857163 0.553659439 0.26308379 -0.59676812 0.1225233 0.47452481 0.39641389 -0.4648496916 -0.432446416 0.25929223 0.48938377 -0.03614696 -0.087619025 -0.409483402 -0.39069390 0.44383724 -0.217291058 -0.06841149 -0.20808586 0.30133475 0.2338089031 0.628743013 -0.21619683 -0.24904089 -0.29348796 0.201532148 0.37954912 0.371373220 0.35506241 0.16613077 -0.1045489108 -0.3541049382 -0.187847376 0.005129543
KEGG_STEROID_HORMONE_BIOSYNTHESIS 0.38438742 0.113162544 -0.45530979 0.357007701 -0.25621878 -0.29318119 -0.1569740 0.14898979 0.39668852 -0.0468902937 -0.117557120 -0.02018489 0.05524139 0.23740098 -0.066581664 0.258410115 0.10847272 -0.13068365 -0.211051369 -0.28866137 -0.15360410 0.38750091 -0.3238802927 0.274917265 0.25281933 0.01163520 -0.01972985 0.521392285 0.25890358 -0.202780567 0.14930619 0.49695425 -0.0003891365 -0.4015589637 -0.319750989 0.216079876
KEGG_OXIDATIVE_PHOSPHORYLATION 0.03439798 -0.068230945 -0.24335287 0.179558503 -0.07748180 0.23899287 0.5355567 0.10928544 -0.58653812 -0.1232948723 0.011594465 0.25516015 0.10959538 0.23121819 0.196992997 -0.214021354 0.13140917 0.22589733 -0.167995266 -0.12327534 0.02643072 -0.11175039 0.0487111545 -0.293168402 -0.43460403 -0.36521148 0.06558919 -0.309035960 0.24113723 -0.186432466 0.25366326 -0.01546476 -0.1003451715 0.2488324612 -0.323304803 -0.197206582
KEGG_PURINE_METABOLISM 0.20191160 -0.108479208 -0.10596002 0.292297651 -0.05290036 -0.02776887 0.3629813 0.19221693 -0.19257010 -0.1570618328 0.049458419 0.10941378 -0.11575356 0.10624767 0.139611752 -0.104415107 0.24845743 0.18074380 0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986 0.14562604 -0.027395894 0.03493636 0.032161754 -0.01145234 0.00244119 -0.1717349277 0.1040248755 -0.158512548 -0.016876129
KEGG_PYRIMIDINE_METABOLISM 0.31268448 -0.315035601 0.02591551 0.453707816 -0.07827502 0.12111801 0.4400906 0.15739138 -0.34124605 -0.0079268025 0.045340682 0.11082758 -0.26167624 0.22159523 0.249023937 -0.267370796 0.21778307 0.26025801 -0.171924064 -0.24608881 -0.26204891 -0.28320893 -0.0131339608 -0.174961467 -0.39051601 -0.27174210 0.21371632 0.004495443 0.07795065 0.141105313 -0.08136747 0.09135035 -0.2760584617 0.3120288128 -0.422743981 0.010521260
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.04284560 0.242702474 -0.16024204 0.043647596 0.40725858 0.02861019 0.0869175 0.08096997 -0.05586613 -0.2040867733 -0.079009204 -0.30416447 -0.02979989 0.11484475 0.310350471 -0.167737512 0.02286110 0.02643017 0.079373530 -0.12361833 0.09011634 0.03828625 -0.2567878942 0.216249675 -0.26035482 -0.15309936 0.26950126 0.340594005 -0.28467469 0.223281462 -0.05508784 0.11421331 -0.0221915154 -0.3103008655 0.128094123 0.236156967
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.24472652 -0.281133287 -0.11156638 0.120281095 0.17443484 -0.21565939 -0.3081781 -0.11343483 0.31456894 -0.1543122886 -0.174461409 0.00981391 -0.39082192 0.15162090 0.304717020 -0.014069234 0.02620582 -0.23568881 0.193879486 -0.13962369 -0.14580659 0.28040853 -0.0968041965 0.295147940 0.20766864 -0.09101975 0.19914336 -0.142750362 -0.06039776 0.529969819 -0.28971540 -0.01846407 -0.0650840198 -0.3562492770 0.352102978 0.244584623
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.46919646 -0.380168943 -0.01773872 0.429812246 0.17364178 -0.20436261 0.3043864 0.34337161 -0.38080508 0.0857564710 -0.259409275 -0.05096080 -0.18249829 0.51288839 0.190289996 -0.436378420 0.26664702 -0.04414401 0.003940629 -0.49894385 -0.19574616 -0.05029689 -0.1798573066 -0.187265879 -0.11896302 -0.27828650 0.06494072 0.013637116 -0.27060418 0.395741143 -0.20169400 -0.05662690 -0.2624484362 0.0223987576 -0.151832657 0.296253623
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.13275992 -0.334172234 -0.25729613 0.213014739 0.16552566 -0.28549989 0.5557899 -0.12594035 -0.32547571 -0.0907632515 0.375179490 -0.05918342 0.18499723 0.52187226 0.300515960 -0.433259137 0.36300112 0.23581480 -0.253354935 -0.24446632 -0.23069885 -0.30728634 -0.1095251897 0.335974432 -0.42786720 -0.35467130 0.05607809 -0.014724657 -0.38384764 0.189365161 0.32880955 -0.10650837 -0.2283860731 -0.0006837462 -0.011463264 0.281658787
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.35031536 -0.131098230 -0.53101140 0.415024947 0.45022902 0.07344530 0.2667975 -0.21350030 -0.37419888 -0.6434244295 0.073570259 -0.16930988 -0.19093678 0.44377540 0.326753030 -0.395315587 0.20165887 -0.22843625 -0.345896575 0.21733136 -0.03379007 -0.33373706 -0.5598750406 0.105668958 -0.11338129 -0.25640184 0.53293944 -0.179140993 -0.15447191 0.309858597 0.28568125 -0.55068386 -0.2164372037 -0.1388932338 0.141542931 0.095210761
KEGG_LYSINE_DEGRADATION 0.18631105 -0.302707855 0.14202963 -0.001457447 0.05052599 0.13664666 0.3353993 0.17015808 -0.15999281 0.0003802554 0.054289069 -0.06841515 0.19332597 0.06780524 0.394846160 -0.308209809 0.06840594 -0.30368912 0.173959126 -0.20656156 -0.14215812 -0.10346628 0.1434771096 0.077612666 -0.18316752 -0.05935752 0.15458897 -0.072955358 -0.26549273 -0.117408842 0.01486245 -0.19612153 -0.3691316847 0.0986933555 0.018713137 0.172759177
KEGG_ARGININE_AND_PROLINE_METABOLISM 0.27398245 -0.007553433 -0.20383827 0.190912564 0.26352645 -0.08892086 0.3364975 0.08336217 -0.15782044 -0.0366667890 -0.011447268 -0.19979109 0.07225283 0.30484966 0.104227507 -0.292574794 0.28948741 0.07959214 0.004233241 -0.25695797 -0.29744163 0.17250236 -0.1975298264 0.243301838 -0.25109237 -0.11660031 0.11820678 0.051556447 -0.24134955 0.339674687 0.03932339 0.11905051 -0.1702678011 -0.1936881912 -0.061558207 0.052832710
KEGG_HISTIDINE_METABOLISM 0.32955287 -0.058544393 0.23401842 0.171291998 0.01579836 0.04289179 0.1478472 -0.19081266 0.10636274 0.0513523626 -0.227789459 -0.12657552 -0.23705948 0.17255355 0.063928642 -0.080957390 0.35225566 0.03053317 0.084445528 -0.09753282 -0.25255017 0.15575959 0.0462057297 0.127088199 -0.15801348 -0.39696091 -0.45105115 0.434357500 -0.03828497 0.050745235 -0.09141518 0.34481527 0.0778549056 0.1205808645 0.113071962 -0.107230492
KEGG_TYROSINE_METABOLISM -0.01013158 -0.196595442 -0.32598629 0.237374402 -0.23250901 0.20262459 0.2232565 0.26627457 -0.23842877 0.1924628476 -0.246173912 -0.11841733 -0.42705595 0.01951022 0.004484624 0.007798831 0.38715574 0.09743186 -0.182999776 0.20096611 0.40982753 0.05350491 -0.3214152163 0.182897748 -0.31135667 -0.45610097 0.33612797 0.127951123 0.29610319 -0.171090713 0.15670333 -0.08207433 0.2424991314 -0.0314562499 0.083631130 0.152278634
KEGG_PHENYLALANINE_METABOLISM 0.18148770 0.461371608 -0.62020227 -0.140393277 0.27692153 -0.20565575 -0.2649484 0.10789494 -0.12695163 -0.1941535369 -0.595583680 -0.09085442 -0.46311485 -0.44379258 -0.093990808 0.280938193 0.09934493 -0.08162794 0.486358071 -0.06639144 0.37934632 0.56113507 -0.1060230711 0.468069197 -0.17744056 -0.17662290 0.14870307 0.649119193 0.19443272 -0.290354517 -0.55479111 0.45091097 0.3370977631 0.1944685634 -0.125721282 -0.096339449
KEGG_TRYPTOPHAN_METABOLISM 0.02655589 0.043109593 -0.31856690 0.098466690 0.13008831 -0.18630463 0.2146807 0.05227151 0.09215733 -0.1502355445 0.007752516 0.06575941 0.14715900 0.31087022 0.208518310 -0.129119060 0.15933118 -0.11659123 0.158404342 -0.40413725 -0.29996492 0.20866768 -0.0003029911 0.127581506 -0.15098840 -0.26429807 -0.09215367 0.330810321 -0.29378958 0.015665134 -0.06172804 0.33048668 0.0406671480 -0.0549421996 -0.009869338 -0.070819327
>
> gbmPar <- gsvaParam(gbm_eset, brainTxDbSets, maxDiff=FALSE)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up -0.3047539 -0.2946860 -0.1834593 -0.5442776 -0.2834175 -0.2788147 -0.3003514 -0.2874994 0.2607199 0.1413387 0.2146940 -0.3180027 -0.4002297 0.1769516 -0.2588480 -0.3482341 -0.2662723 -0.3459269 -0.4173384 -0.1983332 -0.1586231 -0.3486947 -0.3458663 -0.2206452 0.2825297 -0.3877544 0.2093004 -0.2012996 -0.3454799 0.1747717 -0.1457140 0.1895460 -0.2553038 -0.3954264 -0.1289837 -0.3769329 -0.4737155 -0.3632470 -0.3043683 0.2444025 -0.3233087 -0.4249789 -0.3426041 -0.2380239 -0.3075525 -0.3459151 -0.3087816 0.2381330 -0.2643738 -0.2797349
astroglia_up -0.5149583 -0.5410770 -0.4707559 -0.6113382 -0.4302575 -0.3653708 -0.4790737 -0.4724831 0.2019720 -0.5165498 -0.3810421 -0.4003590 -0.3525063 -0.4778482 0.1594521 -0.2744265 -0.4668132 -0.5181954 -0.4725050 0.3496106 0.1632234 -0.5350220 -0.5062797 -0.5565810 -0.2063866 -0.4462150 -0.1671050 -0.4503466 -0.5630672 -0.4053433 0.1609667 -0.1794776 -0.4755774 -0.2128034 -0.1997192 -0.5332830 -0.4417129 -0.4310179 -0.4982304 0.2722387 -0.3527572 -0.4120461 -0.5092322 0.1534758 -0.3638957 -0.2886322 -0.3058095 -0.2268245 -0.3789481 -0.4199315
neuronal_up 0.5535049 0.2417091 -0.2419423 -0.1264513 0.5321516 -0.1907802 -0.3594715 0.3119123 0.4301345 -0.1251531 0.6345184 -0.4761376 -0.4777196 -0.3691534 0.2468458 -0.3802419 0.4236358 -0.4473820 -0.1168248 0.2615203 0.4412960 0.2258959 0.4605784 -0.1201504 -0.2601714 -0.2213066 0.5831010 -0.3449359 -0.3518502 0.1186366 0.1916525 -0.3076000 0.3498210 0.4973920 0.6397865 -0.2787217 0.2572456 0.4607110 0.3686673 0.1846618 0.5245801 -0.3509494 0.3513964 0.5454430 0.1606448 -0.2953076 -0.5303268 0.6995543 0.1475983 -0.1844540
oligodendrocytic_up 0.3317492 0.2491713 0.3353197 0.1965032 0.4766178 0.3696743 0.1739008 0.2837137 0.3965796 -0.2499617 0.4111354 0.3145638 0.6296969 0.3363415 -0.1374640 0.4114245 -0.3041959 0.2647537 0.4139883 0.2318300 0.3873472 0.2032636 0.4537419 0.2660245 0.5308132 0.4464649 0.5707848 0.3329401 0.4571077 0.2958584 0.3318632 0.4968947 0.3523085 0.5364637 0.4087340 0.5468353 -0.1492890 0.4105960 0.5855587 -0.1819342 0.4798445 -0.1856330 -0.1874635 0.4959465 0.5271533 0.2206708 0.2340045 0.2860177 0.1995836 0.1418165
TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up -0.4388712 -0.2984390 -0.2418500 0.2967027 0.2963262 0.5497730 0.2387450 0.3144786 0.3333460 0.2297994 0.2686543 0.2357884 0.3223822 0.2434233 0.4129700 0.3558037 0.2586949 0.2957692 -0.1293295 0.4002767 0.2431737 0.2064763 -0.2054680 0.2098025 0.2378884 0.1979041 0.2823311 0.1955658 0.3445508 0.2594091 0.2529872 0.4826020 0.1815513 0.4318795 0.2885936 0.3123410 -0.3779783 0.1939708 0.1641413 0.1497425 0.2281183 0.1198567 0.3737903 0.2232357 0.2131509 0.2635626 0.2295927 0.2025863 0.3654367 0.3070467
astroglia_up -0.5577897 -0.3009622 -0.4952939 0.3562099 -0.1948617 0.2506709 -0.1956322 0.2980680 0.1473354 0.1866536 -0.4623550 -0.1714237 -0.4221490 -0.1818365 -0.2457673 0.2500337 -0.2661463 -0.1506672 -0.4899183 -0.3467717 0.2013752 -0.1561121 -0.2157769 -0.2982904 -0.3172812 -0.2281312 0.2970433 -0.2815591 0.1634429 -0.1746780 -0.3294734 -0.2707020 -0.3002505 0.3839744 0.2305549 -0.1605050 -0.2294543 0.4619706 -0.1943197 -0.2982120 -0.2123044 0.3634887 0.2863492 0.3384878 0.1948430 0.1395315 -0.2248029 -0.2162429 -0.2067516 -0.3013420
neuronal_up 0.2111547 0.1714030 0.4657383 0.5497687 -0.3946098 0.4963120 0.3352992 0.7175166 0.4972767 0.3710156 0.7631191 0.5344811 0.7969773 0.2856497 0.3129090 0.6442165 -0.2297751 0.4688783 0.7186127 0.1864052 0.1512623 0.4905083 0.5779253 -0.1747120 0.7386962 0.5896950 0.2983598 0.4279023 0.2145936 0.1761452 -0.5754318 0.4795529 -0.6007193 0.6585229 0.2712467 -0.5609244 -0.5409766 -0.5582310 -0.1397818 -0.1699394 0.1369626 -0.2852583 -0.2074379 -0.3609699 -0.4746596 0.2723624 -0.1921239 -0.6249382 -0.1989687 0.4172576
oligodendrocytic_up 0.3666431 0.3008428 0.3834914 -0.2197493 -0.4632601 0.1755629 0.2283133 0.3855686 -0.1581432 0.2212679 0.2711446 -0.1950745 0.2557408 0.2960432 -0.1573391 0.3797065 -0.3338795 -0.2831008 -0.2227159 -0.1671839 0.4939055 0.1723784 -0.2516605 -0.1981382 0.3178961 -0.3937384 -0.2466558 -0.4638286 -0.4636637 -0.2714250 -0.3701235 0.2071280 -0.3779293 -0.3386804 0.2197589 0.2601284 -0.3611962 0.1908298 -0.4231171 -0.3430255 -0.3512123 -0.2820085 -0.3780724 -0.3704518 -0.3216412 -0.3171512 -0.2142009 -0.2771720 -0.1908734 -0.1300848
TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up 0.4009205 0.3415409 0.2219087 0.2208367 0.2603907 -0.1765010 0.2940235 0.2124375 0.4061779 0.4328053 0.2173015 0.3551808 0.2219615 0.4042258 0.3642527 0.3044645 0.3551091 0.4812290 -0.2947330 0.2717050 -0.2072296 -0.2471975 -0.2842497 0.3991259 -0.2766075 -0.1677575 -0.2641184 -0.1595722 0.1984901 -0.2226697 0.1713801 -0.2188904 -0.2579632 0.1518073 0.1637208 0.3756718 0.2550845 0.1295303 -0.2700193 0.2063444 0.1624008 -0.3704812 -0.2729261 0.1962416 -0.1590410 0.3119768 0.2627011 0.2888753 0.2002931 -0.1400612
astroglia_up -0.2684818 -0.2478927 0.4042948 0.2335354 -0.4561683 -0.2852517 0.2751976 0.3726306 0.3118150 -0.2394383 0.1820660 -0.2988110 0.1652119 0.1841336 0.2581383 0.2056429 -0.2597831 0.3690882 0.4820315 0.2887467 0.5403445 0.4579650 0.5444281 0.5331769 0.3394440 0.2194871 0.5238034 0.4465451 0.4552118 0.3171873 0.5092584 0.4264341 0.3355302 0.4395682 0.3572217 0.5354133 0.5529363 0.3635790 0.4608111 0.3641927 0.4291813 0.4496740 0.4566347 0.3510896 0.4412179 0.3601076 0.3276640 0.5528990 0.4514321 0.2932687
neuronal_up 0.4714021 -0.5453959 -0.2184275 -0.6205832 0.3765956 -0.4810052 -0.3898214 -0.3376351 0.4026263 0.2958724 0.1514880 -0.5448607 0.4816556 -0.5156220 -0.5857302 -0.3912544 -0.4810045 -0.4432014 -0.3401462 -0.2069768 -0.1755817 -0.5429475 -0.3473447 0.4293285 -0.1852551 -0.2807897 0.2095081 0.1692813 -0.5953110 -0.4569613 0.4986510 0.6780347 -0.4361162 -0.2657947 -0.4149003 -0.2019748 -0.1825776 0.4705841 -0.3660470 -0.3950770 -0.2875748 -0.3687514 -0.4339034 -0.4137328 -0.4061838 -0.3665761 -0.2886278 -0.4494102 -0.4614783 0.3012511
oligodendrocytic_up -0.2170210 -0.3505377 -0.4033821 -0.4180423 -0.4282208 -0.4921075 -0.3129745 -0.2568446 -0.4508574 -0.3521717 -0.1932037 -0.2401757 -0.4705363 -0.4756500 -0.3939968 -0.4508653 -0.4673510 0.6267838 -0.3869379 -0.1753464 0.1398180 -0.3356724 0.2174792 -0.1909474 -0.4170448 -0.3449788 -0.3789635 -0.3723979 -0.2489271 -0.2955629 0.2563263 0.5062260 -0.3722382 -0.2544347 -0.4120718 0.1481816 0.2266027 0.2624142 0.6390087 0.1041047 -0.3246204 -0.2504649 0.1695500 0.3362893 0.2602318 -0.4512150 -0.2275365 -0.4490874 0.2728064 0.1801245
TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up -0.3141722 0.2699874 0.2219473 0.2091188 0.2345999 -0.2194917 -0.3453076 -0.4238358 0.3549822 0.2340566 -0.2593196 0.1099604 -0.2273672 0.2019316 -0.2041700 -0.1508235 -0.2519564 0.1867464 -0.1965190 0.2585439 -0.3990271 -0.3061357 0.1651281
astroglia_up 0.3922137 0.2846455 0.4656351 0.5682138 0.4886159 0.3895400 0.3730679 0.2343013 0.4820948 0.3943550 0.4396104 0.5514612 0.4772503 0.5054087 0.5478562 0.3711037 0.3050986 0.2872253 0.2808018 0.5497252 0.4051805 0.4516472 0.4085658
neuronal_up -0.4367833 -0.3295978 -0.2846818 -0.4517050 -0.3885191 -0.3608320 -0.3779686 -0.3484378 -0.2868552 -0.5719856 -0.2625708 0.2935293 -0.3335214 0.6340333 -0.4788773 0.5079833 0.1255322 0.2449831 -0.5029271 -0.3891953 -0.3632664 -0.4659142 -0.2670667
oligodendrocytic_up -0.1680797 0.2981662 -0.4332569 -0.2097164 -0.4411032 -0.4515751 -0.1344606 -0.2894701 -0.3966829 -0.3681011 -0.2038674 -0.1537039 0.2336640 -0.2932406 -0.2495044 0.2091980 -0.3179201 -0.3245650 -0.2703005 -0.4534530 -0.4265475 -0.4192150 0.1600080
>
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> leukPar <- gsvaParam(leukemia_eset, cgpC2BroadSets,
+ minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP -0.284185921 0.09894281 -0.09166085 0.15556858 0.018687701 0.21589856 -0.159760678 -0.39128861 -0.26727234 -0.44679630 0.325744327 -0.23951518 0.051302632 -0.278506974 0.04015073 0.347632324 -0.24804097 -0.38938143 -0.15524618 0.19043913 0.02370623 0.068903997 -0.29422954 0.36158458 0.322237127 -0.075044727 0.18750433 0.22546588 -0.150244738 -0.132861970 0.245771407 0.253424577 0.149179429 0.256834003 0.54585089 -0.13771429 -0.381283518
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP 0.074234671 0.28539841 0.54867983 -0.21455850 -0.196029929 -0.25981972 0.473892865 0.08132092 -0.02781303 0.54530761 0.366563615 0.32206336 -0.020333305 -0.304173959 0.16484183 0.025761275 0.04010094 0.12058207 -0.28234199 -0.32765526 0.33755016 0.062136062 -0.17438543 -0.27714732 -0.175368929 -0.068632830 -0.16029136 -0.54312340 -0.457243901 0.063838909 0.284048174 0.451910696 0.065458637 -0.216675403 -0.09964422 -0.46293573 -0.471055266
WINTER_HYPOXIA_UP -0.122226539 0.19658831 0.19027777 -0.19779261 -0.295049369 -0.24808384 -0.216814893 -0.14968164 -0.14439647 0.16117004 -0.263075768 0.24300974 0.212753169 0.219567220 -0.26389007 0.067029667 -0.06856209 -0.08909042 -0.05226506 -0.30733660 0.22533379 0.193092854 0.04216994 -0.27030754 0.146503383 0.248352494 -0.08507045 0.02799035 -0.019718990 0.163757054 0.226094520 0.147465095 0.144632935 -0.177600100 -0.03490205 -0.02579216 -0.201473546
PYEON_HPV_POSITIVE_TUMORS_UP 0.373338180 -0.08195895 0.49691537 -0.35523689 0.073820829 0.08656391 0.257900378 0.52264452 0.40765416 0.46023184 0.085547216 0.57035112 -0.453573874 0.127033813 0.41338035 -0.144148442 0.34650611 0.42161444 0.05076537 -0.50755967 0.06858839 -0.122209941 0.14630225 -0.46393255 -0.297018214 -0.007595085 -0.17430019 -0.34867040 0.238611621 -0.485707594 -0.393180984 0.283583934 -0.117141935 -0.264746769 -0.50063635 -0.42226439 0.030286161
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP 0.034852372 0.17810998 0.33466738 -0.18043537 -0.301630159 -0.25696203 0.069464046 -0.13728252 0.03289923 0.15662255 0.008254385 0.17876533 -0.035728864 0.263860776 0.18841806 0.054449457 -0.05893731 -0.03627519 -0.02106037 -0.30409556 0.26346145 -0.033555920 -0.09904109 -0.31073293 0.196059298 0.041943377 -0.27670124 0.05374531 0.102078549 0.089751050 0.126164281 0.073107504 0.159604038 0.149992036 -0.17339221 -0.12806055 -0.183128694
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP -0.297408395 0.12039801 -0.26428063 0.17004586 -0.039805152 0.09850287 -0.057298350 -0.35386190 -0.16713553 -0.07892505 0.200098274 -0.20933571 0.144977450 -0.026805809 0.09893933 -0.004404619 -0.15285474 -0.30327609 -0.06851817 0.09694832 -0.24544948 0.118722964 -0.34259752 0.15768732 0.172784905 -0.184720574 0.19647116 0.20367723 -0.143437960 0.203937367 0.294431435 0.184358331 0.272106482 0.260812933 0.29031258 0.18633750 -0.058307777
LU_TUMOR_VASCULATURE_UP -0.303485092 0.05954910 -0.08947968 0.17393748 0.055216604 -0.21711694 -0.068811743 -0.36596763 -0.10701941 -0.26356696 0.360410658 -0.07864957 -0.121613155 0.177822010 -0.01104916 0.229093881 -0.18613941 -0.27316309 0.12995187 0.27171808 -0.30894560 0.172438331 -0.30343314 0.37190436 0.180795286 -0.104016386 -0.07390340 0.21484484 -0.372653361 0.272063159 0.146426458 0.292726824 0.073215278 0.236064108 0.12233488 0.30677400 -0.166297976
KORKOLA_EMBRYONAL_CARCINOMA_UP -0.237891606 0.22324873 0.36244453 -0.10961418 -0.136474592 -0.46990350 -0.273764475 -0.16989735 -0.22372057 0.11247316 -0.232337649 0.28697934 0.017986838 0.142356962 -0.07127081 0.189358376 0.18951708 0.36031203 -0.18122486 -0.25323494 0.42996355 0.240702262 0.14655134 -0.29879857 -0.105909705 -0.186176950 -0.23520759 0.11808592 0.123806950 -0.096186587 0.082449346 0.068290275 0.204362056 -0.305158509 -0.18242290 0.07924085 0.050412994
KORKOLA_TERATOMA_UP 0.069466630 0.31282751 0.26793152 0.09145777 0.364378105 -0.01610294 -0.429410344 -0.34268743 -0.49321544 -0.29390567 -0.294556431 -0.43171623 -0.275085564 -0.198360712 0.34983219 0.320807082 0.13961117 -0.13440310 0.10165153 0.12248119 0.32044205 0.106653855 0.01837852 0.25031318 -0.310896163 0.053773795 0.03604947 0.33071217 0.066562201 0.280163027 0.039476681 -0.126383734 0.241910733 -0.323470237 -0.03914776 0.30954031 0.103077314
KORKOLA_YOLK_SAC_TUMOR_UP 0.165072940 0.38624888 0.50530097 -0.37418563 0.006252226 -0.41666427 -0.301013273 -0.13354266 -0.14397323 0.31804861 -0.080548556 0.23290348 0.035345111 0.007931487 -0.09467101 -0.158566311 0.29400647 0.34421179 -0.14156018 -0.16187218 0.22342054 0.257582308 -0.07203685 -0.28296980 -0.390797184 -0.299345198 -0.33442798 -0.05640545 -0.267890012 -0.360997781 0.046532067 -0.038161214 0.260330724 -0.286721001 -0.29560478 0.25567578 -0.058961842
KORKOLA_CHORIOCARCINOMA_UP -0.010233903 0.32695285 0.23409239 -0.44995947 0.110491619 -0.77486388 -0.590305245 -0.30294240 -0.37350003 0.22506301 -0.122120864 0.36713585 0.321071992 -0.025352644 0.18055781 0.006019335 0.33689753 0.01559227 -0.39322807 -0.49057169 0.60777944 0.563917133 0.23716208 -0.44914903 -0.257199360 0.181773354 -0.26429369 0.34875870 -0.418331961 -0.402954949 0.279270709 -0.219024970 -0.073131401 -0.377126885 -0.01449304 0.08204518 0.009841082
KORKOLA_SEMINOMA_UP -0.298212257 0.01080115 0.24405821 -0.15938874 -0.027952932 -0.28780633 -0.247319424 -0.33519149 0.06014085 0.22168793 0.058430886 0.28316538 -0.005576346 0.060208089 0.07375198 -0.081445539 0.16610491 0.42430320 -0.01533883 0.08230093 0.24992576 0.077656272 -0.06562014 -0.16684190 -0.284188016 -0.287282092 -0.16462701 -0.05811647 -0.062401658 -0.099243073 0.073201955 0.067154795 0.267030362 -0.298357838 0.02900301 0.32555350 0.080225727
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP 0.097593813 -0.16794685 0.35151193 -0.23237964 -0.163197206 -0.29950843 -0.006714904 0.34062208 0.09604888 -0.11003744 -0.171064434 0.06587775 -0.266062516 0.220122655 0.33608928 -0.127916894 0.11383392 0.19988434 0.20190981 -0.30021326 0.14299295 0.063923084 0.05677644 -0.28986580 0.038510117 -0.159509213 -0.29388778 0.05765373 0.326704138 0.074522409 -0.274247777 -0.275056415 0.053402889 -0.002107284 -0.34859857 0.03644107 0.208732689
HOLLMAN_APOPTOSIS_VIA_CD40_UP 0.105496299 -0.13988837 0.38579893 -0.24564927 -0.083118397 -0.02283095 0.141139992 0.25611563 -0.05713898 0.01803229 -0.087474542 0.14542629 -0.210191344 0.211687858 0.22093653 -0.133326040 0.06549381 0.18478682 -0.03775017 -0.20148605 0.22321211 -0.059252095 0.01426428 -0.09291203 -0.005412103 -0.025056156 -0.28678304 -0.10392565 0.206300949 0.073580108 -0.204915942 -0.221567934 -0.045463659 0.033396194 -0.24875118 0.01892772 0.157710229
LIU_PROSTATE_CANCER_UP -0.224388256 0.06307335 -0.08241727 -0.04832687 0.189906903 -0.02124567 -0.279030644 -0.27886322 -0.09392327 -0.19792744 -0.029580432 -0.03027978 0.202657103 -0.340883536 -0.03209933 -0.116168855 -0.30287655 0.21450416 -0.04221989 -0.04528200 0.06964423 0.083598831 0.16642355 0.12185052 -0.000928352 0.140595272 0.28592176 0.02379778 -0.071982214 0.154329444 0.077278879 0.239783535 0.316168936 0.045907958 0.11350734 0.06778064 -0.142535169
LIU_SOX4_TARGETS_UP 0.121044935 -0.14068822 0.22940559 -0.01597795 0.061591507 -0.00693642 0.014199778 0.30911203 -0.08600822 -0.02038572 0.114287917 -0.21978031 -0.226307014 -0.023607467 0.29166627 0.064022632 0.06822989 -0.07130524 0.23335358 0.06981417 -0.11573705 -0.291602661 -0.13629614 -0.03270145 0.024218801 -0.013336764 -0.10693992 -0.16558042 0.190828338 0.225771717 -0.229823064 -0.164944356 -0.179080910 0.177092706 -0.17646028 -0.18791880 0.240962021
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP 0.062841657 -0.18362789 0.29336781 -0.18594491 0.154299300 -0.05557008 -0.083102532 0.04576576 -0.09217560 -0.19543518 0.055196463 -0.04809592 -0.052719541 0.107250567 0.17234102 0.220352187 -0.04953385 0.24873127 0.13828440 0.19314948 0.04975678 0.049538498 -0.06477196 -0.06226135 -0.098276136 -0.129915554 -0.19707557 0.02496088 -0.051271962 0.052870430 -0.073226448 -0.184972633 -0.012686096 -0.071808834 -0.27150226 0.27912570 -0.135303937
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP -0.094846112 -0.07207493 -0.02804641 0.03696695 -0.086436392 -0.08397341 -0.068172639 -0.05763452 -0.02656466 -0.17775526 0.258308865 -0.14822566 -0.145150486 -0.039994112 0.10916677 -0.090893212 0.03680901 -0.09371656 0.11806513 0.17785724 -0.11045327 -0.058180594 -0.31826977 0.09626481 0.143735941 -0.160260444 -0.06107374 0.08258827 0.034945942 0.261716811 0.008073164 -0.089058343 0.056294586 0.251527056 0.01348282 0.28709952 0.102083930
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP 0.074340051 0.02857125 -0.24003150 0.30715667 -0.010403308 -0.10045962 -0.159844495 -0.22324560 0.02880624 0.11715699 0.077777052 -0.17990167 0.106011986 -0.179976522 -0.09660455 0.026469354 -0.12555729 -0.17002077 0.19363609 0.07413777 -0.34472957 0.071120620 -0.23684660 0.25225819 0.214521242 -0.165874245 -0.03452474 -0.02439650 -0.180590309 0.011098030 0.114305528 0.052961087 -0.068405608 0.293293442 0.24643595 0.09297256 -0.030979738
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP 0.005014724 0.08111308 0.26913235 -0.09552045 -0.450228901 -0.20835559 -0.341832089 0.08934729 -0.33423215 -0.07570491 -0.227456658 -0.31425832 -0.075046342 0.101225498 -0.22803411 0.359148102 0.25779762 -0.50524646 0.12655983 -0.08326589 0.16277302 -0.238058161 -0.17065282 0.06861909 0.125783171 -0.153453577 -0.06888951 0.35891268 0.238976848 0.449575492 -0.397721447 0.129949315 0.063354595 0.344276854 0.21919705 -0.02084416 0.446602851
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP -0.086490808 0.42662285 -0.06186335 0.19254225 -0.147417154 0.23175825 0.491914629 -0.11696009 0.01145265 -0.18617542 -0.098643515 -0.08071038 -0.040838732 -0.284554435 0.44402053 -0.167965862 -0.06796364 -0.12183172 0.37256760 0.34632681 0.01477953 0.154501865 -0.14155636 -0.17148626 0.040841265 -0.199318164 -0.03141871 -0.02556187 -0.194745034 0.111576773 0.299019277 -0.246935585 -0.304924920 0.249744542 0.16874813 -0.28320150 -0.409684665
FRASOR_TAMOXIFEN_RESPONSE_UP 0.095102205 0.13613061 0.27963248 0.10696680 -0.201251938 0.04440738 0.039666191 0.08072985 -0.30347286 -0.13117213 -0.163829152 -0.08811162 0.130289925 -0.269491251 0.04481561 -0.129982372 -0.09261704 0.05779261 0.20931794 -0.11293941 -0.08782228 -0.154603301 -0.10942582 0.03255269 0.068908002 -0.134879788 -0.11865894 0.03929191 0.105215621 0.144775760 -0.132818191 -0.126161041 0.046198277 0.066790819 0.10784581 0.14897625 0.103889267
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP -0.093263740 0.24451532 -0.30875436 -0.01171828 -0.077592391 0.06977365 -0.047698353 -0.25543630 -0.16734657 -0.29943342 0.138659259 -0.24677548 0.008316094 -0.097198227 -0.07991562 0.237943766 -0.08176618 -0.34607119 0.18984664 0.28121888 -0.29765020 0.006609358 -0.17838613 0.18555511 0.093828022 -0.218609231 0.17434097 0.06804717 -0.095062879 0.199580074 0.321860622 -0.008284166 -0.001916854 0.183088620 0.25305607 0.13585610 0.034581179
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP 0.203957767 0.12189117 0.38492132 -0.24300464 -0.090523098 -0.19966713 0.102728363 0.04976671 0.18283638 0.30437400 0.148109727 0.24724848 -0.327248458 0.129670458 0.33143975 -0.086102559 0.10335793 0.20068518 0.03773511 -0.23454620 0.13617294 -0.090673447 -0.26073243 -0.38875239 -0.054723088 -0.050551494 -0.23180710 -0.12601589 -0.001883262 -0.007476349 0.072573918 0.189048383 0.090254301 0.187420576 -0.31338258 -0.10912037 -0.247410905
WATANABE_COLON_CANCER_MSI_VS_MSS_UP -0.156524705 -0.00167507 -0.10689295 0.36427412 -0.010218876 -0.06496857 -0.269749963 -0.27745767 0.02119152 -0.21830558 -0.196574719 -0.35120814 0.269162954 -0.142483756 -0.26808257 0.038724466 -0.07004319 -0.11588327 -0.10292213 -0.06427425 0.25284346 0.283925446 0.01040659 0.32549432 0.230151042 0.409316724 0.37175290 -0.27673142 -0.066751401 -0.078279396 0.099369827 -0.165196141 0.013360644 0.168730310 0.23632001 -0.18337713 -0.329485400
>
> proc.time()
user system elapsed
70.32 8.71 79.29
GSVA.Rcheck/tests/test_gsva_newapi.Rout.save
R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> ## 2023-11-10 axel: simple test script for method GSVA, new API
>
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
expand.grid, I, unname
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db
> library(GSVA)
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 1.4171739 -1.3444519 -0.99052898 0.4203395 1.30716224
g2 -0.7281951 0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754 0.09779699 -0.6792548 -0.09124045
g4 1.0735382 1.3156255 0.15588330 -1.8079608 0.48531108
g5 0.7229884 -0.9162342 1.93982245 0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> gsvaPar <- gsvaParam(X, gs)
> gsva.es <- gsva(gsvaPar, verbose=FALSE)
> dim(gsva.es)
[1] 100 30
> gsva.es[seq.int(min(nRowsToPrint, nrow(gsva.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 -0.108156444 0.16592613 -0.143808928 0.11391879 -0.08600850 -0.1734242744 0.178707342 0.017723667 0.094198786 0.103231011 0.098990086 0.056687452 -0.19582109 0.012296862 0.162223446 -0.114766326 -0.293330673 0.126367035 0.228829622 -0.14884956 0.026620947 -0.301784054 -0.30631599 0.235331985 0.04638816 -0.1100099596 -0.0999704513 -0.046424755 0.293447378 -0.17344608
gs2 -0.078540545 0.19300391 0.079182716 0.07049058 0.04007773 0.1715072044 0.203277577 -0.081465590 0.233451158 -0.280324459 0.037382517 0.025061259 0.10845168 -0.059159170 0.026844586 -0.179610527 -0.014413382 -0.006820970 0.160768137 -0.03932893 -0.108749046 -0.282019527 0.08605189 0.088382420 0.06394081 0.0207049280 0.2183498851 0.084518747 -0.272555793 -0.17000646
gs3 -0.012507633 -0.25351738 0.102368361 0.03512929 -0.04994980 0.2133058738 0.039178136 0.191682501 -0.398094428 0.343111543 -0.076791958 0.119069468 0.20772960 -0.421116272 0.459538877 -0.026465562 0.049041138 0.038384015 -0.227781747 -0.09134458 -0.514150386 0.102494298 -0.20024782 0.058491931 0.31836609 0.0290482835 -0.1935787866 0.254416177 -0.017322981 0.13715416
gs4 -0.083248846 0.02946102 -0.042556750 0.08145113 -0.05401867 0.1055847509 -0.158661388 0.009278808 -0.107756958 -0.016141791 -0.033233344 0.016122676 -0.08342913 -0.003621483 0.141048462 -0.001454018 0.129386313 -0.062100704 -0.110927318 -0.16530100 -0.059697155 0.032076675 0.03158162 0.038234047 -0.03942766 0.0886365597 -0.0782910850 0.014516781 -0.046885905 0.20075530
gs5 0.129917233 -0.14323749 -0.172890947 0.13411529 0.09628743 0.0265475253 0.050870369 0.174122516 0.081836827 -0.011085820 0.023089550 0.056006287 -0.07140253 0.055193034 -0.091548680 -0.149492965 0.037312222 0.002985924 -0.144101863 -0.01888358 -0.065961297 -0.132468115 -0.06377434 0.028402402 -0.07610908 0.0853809151 0.0806035221 -0.015568714 -0.047153650 0.01778386
gs6 -0.284972014 0.13823428 -0.210772112 -0.05757943 0.10388699 0.1439391564 0.109157571 0.077447106 0.001144118 0.181326976 -0.019716350 -0.006386486 -0.06006467 -0.189315716 0.005405993 -0.001953525 0.006055122 0.159361735 -0.089341440 0.02743543 0.000728224 -0.178928406 0.19578172 -0.036394549 -0.07703071 0.0784321711 -0.0863070990 -0.033617568 -0.088131880 0.09008523
gs7 0.028701964 0.23235456 0.119915418 -0.01970966 -0.13698294 0.0031401764 -0.218020511 -0.195273449 0.038952752 -0.232984107 0.037413398 0.092363954 0.18259907 0.053162383 0.097674825 -0.128073348 0.073567722 0.115641271 0.030537867 -0.13049139 -0.057022525 0.056026838 0.06828574 -0.001000666 -0.06071745 0.0039744122 -0.0005585096 -0.009440488 0.080790372 -0.09940113
gs8 0.006333045 0.01460128 0.136198133 -0.07889863 -0.11123825 0.0387444491 -0.002037746 0.040187847 -0.121686486 -0.095484760 0.052264970 0.150236692 0.04926308 -0.109888308 0.100412242 0.146400621 -0.156050604 0.018922498 0.067657595 -0.05343596 -0.068927042 -0.080941576 0.07501949 0.007660285 0.16079137 -0.2682601362 0.1012140737 0.042776107 0.002111495 -0.05482992
gs9 -0.175865699 -0.19690763 0.060751759 0.18933359 -0.25345038 -0.5016097134 -0.138854281 -0.543295516 -0.263543869 0.275493131 0.127068488 -0.189846149 -0.25784051 -0.094258279 0.079039460 -0.165487585 0.343543465 0.357424759 0.292115383 -0.02178526 0.058171774 -0.034552813 0.23880691 0.043569142 -0.02980941 0.2945856247 -0.0219706361 -0.176772536 0.532204432 0.15142975
gs10 0.098112170 -0.35611542 -0.056579211 -0.21958226 0.08809195 0.0009137342 0.405507850 -0.115481827 -0.187608357 0.275280555 -0.119567715 0.109071314 -0.25466878 0.000375529 0.367963754 0.188641874 -0.079209335 0.256239935 -0.125622141 -0.11854834 0.255106701 0.471876454 -0.37385722 0.223837887 0.02289076 -0.4287911223 0.0067681070 -0.240476346 0.088671730 -0.17764056
gs11 0.098198198 0.25911849 -0.038035464 -0.21771367 0.50403680 0.4428564710 0.303629955 0.175137764 0.098749107 0.336354436 0.130586418 -0.052651015 -0.20599477 -0.223219535 -0.250927738 -0.509205728 -0.444857809 -0.045479124 0.088547534 -0.02722749 -0.099107700 -0.092392768 0.05594057 -0.069222681 -0.02071750 -0.5973180441 -0.1580304020 0.577149382 0.298070860 -0.07458713
gs12 0.096490065 -0.02605933 -0.022030360 -0.13719093 0.02682772 0.0434813048 -0.028867424 0.014475285 0.133723333 0.034558185 0.137695531 -0.258037193 -0.02835015 -0.064346101 -0.026710216 -0.269826308 0.021532017 -0.047943462 -0.022440279 0.16687604 0.055835937 0.023685654 -0.06486901 -0.020025683 0.02178566 0.0480895384 0.1113867112 0.059878337 -0.055779061 0.06729589
gs13 0.223982459 0.20679601 0.258716670 -0.20136940 -0.20071529 0.2464442479 0.258963232 -0.110149641 -0.089442650 0.205739275 -0.165291846 -0.150888458 -0.15226578 -0.404364664 -0.005312768 -0.100572023 -0.220803462 -0.043370760 0.309185329 -0.08715961 0.326811093 0.080713114 -0.10705436 0.116977351 0.19046277 -0.1469583728 0.1367810954 -0.242162288 -0.021163531 -0.29632096
gs14 0.024001674 -0.26723135 -0.398236422 0.24294428 0.04991522 -0.1433770344 0.399168882 -0.248011836 -0.121856855 -0.141859978 -0.080548602 0.105372091 0.28663719 0.303516623 0.320574969 -0.044182057 -0.177554197 -0.058580934 0.063071784 0.11623764 0.096538164 -0.055513833 -0.42073250 0.001550673 0.16488985 0.0464015474 -0.0156188987 -0.085775207 -0.160086709 0.12477191
gs15 0.107236756 0.02674424 0.186569862 -0.12214378 -0.06518532 -0.0612943018 -0.111903203 0.049803938 0.044035633 -0.049752082 -0.024069020 0.205529366 -0.10569735 0.002119758 -0.140742436 0.185481189 -0.005853900 -0.101479169 -0.001425559 0.08308067 0.020882554 0.051697561 0.05197634 0.276490515 0.09494653 -0.1604533503 -0.1106884939 -0.115292890 -0.212477678 -0.04261664
gs16 -0.189661090 0.18212481 -0.194291062 0.11967900 -0.10434220 -0.1191397416 0.039057392 -0.039343595 -0.060222683 -0.067506938 -0.160259179 0.001722109 0.14378774 -0.013559159 0.165627072 -0.022929924 -0.032725397 -0.021268004 -0.036164578 0.04105859 0.054069320 -0.023626997 0.01312951 -0.066479935 0.03594310 0.0510113983 0.0168947880 -0.006306806 0.182001699 0.08182702
gs17 -0.224154710 -0.06839924 0.011942989 0.06596303 -0.01898285 -0.0787236017 0.262432764 0.128350415 0.107171841 -0.036418415 0.004430908 -0.152391953 0.13910575 -0.034949755 0.129033846 -0.096575805 0.027781998 0.086966986 -0.057041784 0.06413185 -0.088718911 0.119981085 0.07640730 -0.116205119 -0.19211361 0.0949234199 -0.0301489984 0.007364308 -0.021454055 -0.05405507
gs18 0.144462699 0.15190319 -0.005644637 0.13442504 -0.06851005 -0.0650767309 0.132965207 -0.072143414 0.065609258 -0.169604968 0.149226527 -0.127080390 0.15127334 0.001524110 -0.096672404 0.138052662 0.156721335 -0.113260460 -0.055010361 -0.11281271 -0.081498926 -0.062627336 0.01138976 0.083051492 -0.11650835 -0.0644334115 0.0158668194 -0.035534584 -0.216520795 0.25451909
gs19 -0.114727405 0.11606640 0.014639537 -0.04539144 -0.15632885 -0.3008348682 -0.045227873 0.057911106 0.077993588 0.122127072 0.004180167 -0.010181304 -0.13058749 -0.017522472 -0.063018173 0.096067773 0.059813582 -0.042255247 -0.110140982 0.28341206 -0.057751403 -0.062970017 -0.26428505 -0.087882907 -0.06031966 0.2005231419 0.0555096129 -0.119697294 0.158883568 0.13631818
gs20 -0.250434807 -0.04667705 0.049213711 0.05304980 0.15123353 0.1091531262 0.061807069 -0.184158384 0.116516282 -0.024996495 0.050439116 0.062684587 -0.03915131 -0.056457080 -0.298840942 0.163262104 -0.029174994 0.169067340 0.055693074 0.03338657 0.068733916 0.047318574 0.05085801 0.007052938 -0.13510237 -0.0802436967 -0.0251620082 -0.048587104 -0.071021904 -0.04269538
gs21 0.135378868 0.16802591 -0.029364914 -0.05595578 0.06148837 0.0971278669 0.093694989 -0.069804459 0.025767351 -0.016170741 -0.101534883 -0.120160395 0.04062725 0.048721679 0.095192931 -0.186471874 -0.048112890 -0.212895052 -0.006971640 -0.06755367 -0.127602218 -0.002382844 -0.01605748 -0.001335954 -0.11991648 0.2219113569 0.1352495887 0.023381243 0.045687474 0.09964681
gs22 -0.163680317 0.18690317 -0.148456673 -0.05079516 0.24365056 -0.0822628950 0.098769260 -0.142649660 -0.444454723 0.065727715 0.247342235 -0.167215276 0.14197399 0.112681184 -0.092957822 -0.152497158 -0.190680030 0.035186284 -0.035122161 0.07290296 0.002562072 0.032535170 0.26649228 0.318514935 -0.22440917 -0.0178361034 -0.3138866671 0.416817320 -0.314242601 -0.02772554
gs23 0.018766631 0.11521514 -0.014809625 0.06153311 0.12707575 0.1281180662 -0.064456890 -0.030536563 -0.129612935 -0.015034995 0.129955588 0.057111134 -0.22165829 0.160845001 0.108799691 0.090243195 0.008299278 0.041996865 0.155112600 -0.08959788 0.079998925 0.013571384 -0.27985106 -0.134362071 0.05587958 0.0900157601 -0.0306708210 -0.124824057 -0.125258066 0.03409850
gs24 0.389869244 0.28790219 -0.049088266 -0.14811747 -0.19067680 -0.3358219719 -0.236811755 0.135616593 -0.238985451 0.206904619 0.248194834 -0.112405472 0.09072771 -0.142415602 -0.383217061 0.363554498 0.187395921 -0.327457108 -0.592050113 0.15802933 0.479729800 -0.150610477 0.28243874 -0.202986917 0.12126635 0.0007700638 -0.0280707676 0.049077412 -0.212219932 0.12363971
gs25 0.093907002 -0.08177613 0.137542184 0.01817976 -0.07335024 -0.2779884851 -0.010150488 -0.109990320 -0.023037802 -0.006390004 0.088013029 -0.003651291 -0.16541049 0.090206786 -0.091065047 0.089689390 0.061729248 0.223324387 0.050045901 -0.08299866 0.221155832 -0.246784249 0.32074709 0.037550027 -0.16709326 -0.1213934826 0.1061837744 0.016007278 0.065201658 -0.19524119
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+ grep("^REACTOME", names(c2BroadSets)),
+ grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- gsvaParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+ minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS -0.14418012 -3.133817e-01 -0.391171673 0.21340339 0.398980386 -0.03179434 0.17524757 0.26705934 0.196519789 0.07076882 0.0145998761 0.27413667 0.083361420 -0.10575923 -0.189608055 -0.30624818 -0.25363521 -0.371666584 0.131382543 0.122449569 0.19101441 -0.452577261 -0.23105310 0.10274129 0.13624827 -0.007124138 0.15976388 -0.102152201 -0.19832123 0.202573385 0.378578854 0.288352608 0.0016120367 -0.36268281 0.110141001 0.255205365
KEGG_CITRATE_CYCLE_TCA_CYCLE -0.20263269 2.546732e-01 0.012685194 -0.23423639 0.166963123 -0.19060735 -0.09504444 0.02350579 0.252153864 -0.29870033 0.3426900775 0.11865360 0.158070942 0.43950013 -0.113554675 -0.41027161 -0.51496205 0.101464045 0.023147027 0.213518494 -0.29129288 -0.365361233 0.19537441 0.34046332 -0.29053602 -0.136804277 -0.03945536 -0.046177552 -0.15861718 -0.197363503 0.005305269 0.139063426 0.3753961988 -0.11672606 0.399275124 0.081808177
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.13384996 -3.426199e-01 0.011055653 0.10473591 0.533196442 0.08319882 -0.07286230 0.33986046 0.183712674 -0.02112598 0.3436817431 0.14970027 0.045619795 0.34106103 -0.319187004 -0.12337277 -0.52047602 -0.079296210 0.246091695 0.007442165 0.29667112 -0.493628865 -0.37567090 0.04398852 -0.10380781 -0.066433829 0.07248245 -0.134640505 -0.28388477 -0.007933863 -0.010660832 0.409249866 -0.0593083889 -0.20730184 0.135344012 0.328985231
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS -0.04814412 2.649390e-01 -0.247781616 -0.57051071 -0.151893395 -0.12257602 -0.22484133 0.15415444 0.170044654 -0.41770107 0.4059486427 0.32600904 -0.337637004 0.45224654 0.240860923 -0.52860069 0.06878373 0.238734193 0.199127444 0.197382585 0.19194776 -0.280713555 -0.14573199 -0.07489534 -0.17115751 -0.356340540 0.19199016 0.464332824 -0.30954147 0.066784875 0.107764195 -0.244087607 -0.0038072528 -0.15577831 0.159465388 0.173314410
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM -0.05277464 -2.559473e-01 -0.272606595 0.02654463 0.466256330 -0.07516578 -0.08827428 0.17940166 0.175438074 0.08335115 0.1949276528 0.03263319 -0.037187373 0.21769233 -0.056026638 -0.21875825 -0.41789351 -0.167172773 -0.116119580 0.028778964 0.18475990 -0.006106045 -0.35983263 0.04835565 0.13058334 0.320582420 0.14792337 -0.356458053 -0.32573808 -0.200330955 0.256816456 0.243425591 0.1799096212 0.04042810 0.078246331 0.111827102
KEGG_GALACTOSE_METABOLISM -0.51060398 -3.263793e-01 -0.339445527 0.18058711 0.590147665 -0.05433206 -0.02631533 0.01150479 0.112418121 0.20086931 0.0758757516 0.18135031 0.172899748 0.09960453 -0.419887121 -0.30998273 -0.41031657 -0.552555465 0.134889700 0.312990925 0.40442648 -0.314101297 -0.45866474 0.24674708 0.36744079 -0.300764693 0.46807677 -0.119986976 -0.47812839 -0.137744193 0.179487063 0.362685887 -0.1178698280 -0.27717714 0.333123866 0.570589012
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.39533716 1.058190e-01 -0.055948980 0.32042238 0.117469296 -0.47857258 -0.27397801 0.48975038 -0.092440191 -0.05795173 -0.0744286061 -0.21729660 0.193086799 0.31390769 0.038143586 0.04976352 0.06941386 -0.243260211 -0.075892533 -0.136936205 -0.70456483 -0.248431863 0.04441643 0.16407617 0.10523266 0.201548537 -0.63041976 -0.064796304 -0.42586995 0.071454531 0.327254119 -0.007811551 0.2006101479 0.02592733 -0.340917460 0.307433176
KEGG_FATTY_ACID_METABOLISM 0.03299573 1.864144e-01 0.209909423 -0.24436698 0.207945636 -0.12244431 -0.23816823 0.49912101 0.388462885 -0.20945911 0.0991996326 0.28644900 0.027816218 0.13251193 -0.076840810 -0.35401475 -0.26281629 0.022061212 0.092216454 0.131207009 -0.32302048 -0.043107375 -0.17671170 0.13894499 -0.29064351 -0.119433589 -0.42265454 -0.103764267 -0.09629923 -0.114672086 0.246246155 0.137119878 0.4886075270 -0.07587824 0.017144468 0.033774833
KEGG_STEROID_BIOSYNTHESIS 0.19815359 -1.774636e-01 -0.495105675 -0.25914877 0.190294265 -0.32446562 0.40274807 0.55575502 0.334577780 -0.30738356 0.0995344990 0.02714295 -0.341505856 0.33481474 0.483575947 -0.46782536 -0.41070981 0.363247663 -0.316476327 0.186672062 0.06775463 -0.460614122 -0.03811347 0.10403630 0.19161113 -0.276517655 -0.31751788 -0.335291201 0.04610323 0.498441393 0.203641470 0.258537460 0.1025848927 0.32986280 0.106728771 0.044375942
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS -0.22772338 3.313823e-01 -0.045122587 0.34604215 -0.326387527 -0.37238068 0.38109784 0.50612839 -0.279733901 -0.46710624 -0.3566433892 0.38150788 -0.160181485 0.32343792 -0.389633800 -0.04093348 -0.34781666 0.439898619 -0.553153746 0.333311581 -0.41569720 0.089984351 0.11640121 0.49616048 -0.18515617 -0.288891006 -0.25307258 0.488505183 0.48932043 0.685621131 0.405112800 -0.410676806 0.0705999647 0.46798357 -0.050407919 -0.059580749
KEGG_STEROID_HORMONE_BIOSYNTHESIS 0.36585090 -4.158145e-02 -0.314872488 0.36177011 -0.117186424 -0.57565233 0.06555161 0.12421684 -0.154537531 -0.03651661 0.2548932547 -0.25983105 -0.191491808 -0.01727654 0.007925232 0.20173611 0.07385251 -0.151691776 -0.174246389 0.170112989 -0.31138189 -0.287770962 -0.32224067 0.25539717 0.10328113 -0.240352841 -0.02844086 0.115892938 0.20532852 0.092026010 0.444749927 0.138675375 -0.1017217201 0.19796954 -0.321674802 0.386149959
KEGG_OXIDATIVE_PHOSPHORYLATION -0.44614351 4.066706e-01 0.315683836 -0.38414333 -0.062919018 0.19858654 -0.22582769 0.04161922 -0.079644512 -0.05102341 0.3664592628 -0.09619084 0.197886790 0.31353680 -0.184933831 -0.36350759 -0.30233809 0.313796606 0.236200087 -0.322015323 -0.29790565 -0.196993574 -0.08707882 0.26462100 -0.24626717 0.241984062 0.12731683 -0.209160519 -0.13913537 -0.164019798 0.003657569 0.174518566 0.2846868562 -0.03739754 0.351418754 -0.151465743
KEGG_PURINE_METABOLISM -0.12658061 6.074446e-05 0.109942629 0.02507931 0.152633778 0.20438698 0.05049747 0.08805693 -0.163334045 -0.09018816 0.2671088095 0.13157027 0.002135794 0.19941825 -0.014318164 -0.19467600 -0.19570945 0.160038352 -0.003976608 -0.159354533 0.04953516 -0.237144513 -0.19729598 0.06518253 -0.20013531 0.065168510 -0.02813078 0.001056042 -0.03466977 -0.006764599 0.054072961 -0.010634495 0.1220901659 -0.14216130 0.002592869 -0.079175937
KEGG_PYRIMIDINE_METABOLISM -0.08169375 2.124920e-02 0.237112503 0.02740654 -0.007840300 0.24898451 -0.04095103 0.23335111 -0.156235016 -0.16193850 0.2906078400 0.19091514 -0.095748971 0.19881417 0.039922114 -0.17823010 -0.14678724 0.256232748 0.020947130 -0.088582706 0.16161796 -0.307232427 -0.08240158 0.03008501 -0.30460678 0.090542640 -0.09034804 -0.174657514 -0.09426947 -0.129635921 -0.040660453 -0.066351934 0.3336055751 -0.05856322 -0.032156131 -0.179871004
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM -0.13254287 -6.225182e-02 -0.134319540 -0.15729012 0.026834849 -0.22343907 0.14168564 0.30713913 -0.125172326 -0.17862058 -0.1731094263 0.30055821 -0.085420317 0.09882301 0.193697084 0.31425985 -0.31600195 -0.125372528 0.295397875 0.180199556 -0.20500280 0.058617241 -0.14777995 0.05091438 0.12367397 -0.040310943 -0.08013473 0.182346297 -0.10198293 0.197362551 0.285434513 0.083269169 -0.3708006909 -0.06111266 -0.243366412 0.222746237
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.10719371 -4.606961e-01 -0.180567057 0.09540174 0.245012608 -0.15656927 0.22420420 0.05451998 0.279637623 0.13353399 0.0588075025 -0.29202943 -0.043946876 0.01212064 0.153895823 0.41802493 -0.13778592 -0.372235469 -0.406109789 0.283133835 0.19519783 -0.020078578 -0.26407215 0.12285472 0.26704639 0.059250879 0.04897781 -0.250007490 -0.05255973 0.087369877 0.196707759 0.202125900 -0.4079062250 -0.14271079 0.201471466 0.148775715
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.31199860 -1.470030e-01 0.003351767 0.19314634 -0.069733318 0.03818098 0.14330053 0.29773728 0.199561609 -0.18575435 0.2414974155 0.26605667 -0.291208656 0.16923947 0.350632975 0.15181300 -0.22743772 -0.019995533 0.165918443 -0.282999158 0.23210130 -0.390498560 0.09366624 -0.22502795 -0.10851096 -0.372625112 -0.43938185 0.172251073 0.03236597 0.169871903 -0.116676657 -0.006200565 -0.2279015972 -0.18233790 0.215082562 -0.127529151
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.13690035 3.114732e-01 0.066312869 -0.42482813 -0.090282754 0.17692622 -0.19729696 0.34694241 0.407012719 -0.49732087 0.4128185814 0.21841977 0.209032500 0.22079194 0.098804076 -0.28545919 -0.23815839 -0.180999045 0.227212036 0.266627679 -0.26343085 -0.365422361 -0.24682867 0.09025547 -0.26797947 -0.355998344 -0.48059599 0.287997010 0.04787260 0.218397773 0.054137782 -0.098018435 0.3267593437 -0.45818263 0.271972064 0.296388858
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.21018404 3.311632e-01 -0.305891231 -0.40884425 0.154601400 0.29113672 -0.24105148 -0.24181442 0.181954325 -0.58092775 0.4049453421 0.24614645 0.133009367 0.50265059 0.272676320 0.03717033 -0.02236702 -0.145501442 0.138011286 0.443984308 0.39650468 -0.290692301 -0.12632929 -0.19057616 -0.07228556 -0.257796347 0.05090257 -0.239289854 -0.27079693 -0.411150458 0.112237525 -0.264314957 -0.4438365768 0.26411102 0.709862664 -0.016572984
KEGG_LYSINE_DEGRADATION -0.05052662 1.114498e-02 0.229382702 0.09046133 0.038741982 0.28814839 -0.18110222 0.18668860 0.200429660 -0.15730855 0.2122002799 0.15678305 0.291243079 -0.09136060 0.075543036 -0.20498916 -0.11109630 -0.119030450 -0.042852292 0.236306523 0.07759842 -0.290175631 -0.01746742 -0.21890493 -0.20792480 0.077495323 -0.27615714 0.039431840 -0.12276895 -0.053898732 -0.080541817 -0.016639943 0.0009973473 -0.40134082 0.137262457 0.007682097
KEGG_ARGININE_AND_PROLINE_METABOLISM -0.22800596 4.906206e-02 -0.042335265 0.01804139 0.185198410 -0.31622084 0.33887630 0.14716659 -0.125964421 -0.04372424 -0.1317531626 -0.23684263 -0.084937438 0.12230128 0.041463950 0.01888723 -0.23867163 -0.418034734 0.100108084 -0.024241225 0.06662724 0.062701077 -0.18005295 0.28126338 0.26487393 0.117918976 0.03282485 -0.267823209 -0.11043893 0.310700224 0.208244241 0.293517379 -0.1408712737 0.08681285 0.022305834 0.089895339
KEGG_HISTIDINE_METABOLISM 0.36390137 2.365551e-01 -0.116603139 -0.05003836 0.327736448 -0.21045969 -0.09444006 0.07411204 0.004241093 -0.21347825 -0.2759296517 -0.09004815 -0.220892221 -0.04865282 0.223799615 0.07800378 0.10695352 0.008719129 -0.157708191 -0.206105926 -0.07079359 0.329843813 -0.03292310 -0.12534816 0.15073847 -0.369373567 -0.44170643 0.302626017 -0.35207965 0.319661614 0.084963193 -0.328337412 0.0562137944 -0.01801214 -0.140975452 -0.224081075
KEGG_TYROSINE_METABOLISM 0.20007757 1.721769e-01 -0.037643348 -0.19625928 -0.075882501 -0.12591313 0.33248542 -0.07760137 -0.191628836 -0.18678014 0.0004931861 -0.41470470 -0.197618861 0.44585904 0.460970463 -0.23734373 0.06323644 0.447147523 -0.339999748 -0.263094997 0.32393110 0.148291697 -0.02476993 -0.16845439 -0.05628810 -0.228433500 -0.09241908 0.205241359 -0.14005676 -0.123163041 0.280135889 -0.404510468 -0.0076082103 0.41987347 0.046111365 -0.109788331
KEGG_PHENYLALANINE_METABOLISM 0.14876060 3.091885e-01 -0.425309307 0.03290077 0.007314721 -0.44139027 0.41683218 0.00264260 -0.665142859 0.33683691 -0.1354678721 -0.56429899 -0.339302707 0.23461582 0.388641234 -0.14178018 -0.13963600 0.402700359 -0.060552296 0.198533242 0.30608114 -0.367173008 0.39977893 0.09861950 0.19457836 -0.450408082 0.02414787 0.419408775 0.14007478 -0.167643347 0.038509810 -0.118899152 -0.4538199574 0.58568820 0.155660090 -0.409252364
KEGG_TRYPTOPHAN_METABOLISM 0.02771378 7.276144e-02 0.164993365 -0.04842795 0.275480475 -0.39691784 -0.07428901 0.25507776 0.187930224 -0.16961352 -0.0772668699 0.10285172 -0.067196121 0.10898541 -0.204308026 -0.07494849 -0.14783141 -0.200577850 0.338704351 0.030157577 -0.38063449 -0.187786425 0.04954516 -0.07650680 0.08969431 -0.024503220 -0.28162674 0.105474846 -0.15358250 -0.063342825 0.059069680 -0.027357901 0.4168932938 0.08101763 -0.197098915 0.014085911
> pickrellPar <- gsvaParam(pickrellCountsArgonneCQNcommon_eset,
+ canonicalC2BroadSets, minSize=5, maxSize=500,
+ kcdf="Poisson")
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esrnaseq)[seq.int(min(nRowsToPrint, nrow(esrnaseq))),]
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.22920126 -0.264187722 -0.37401687 0.291350766 0.17081880 -0.45702585 0.5003620 -0.09626897 -0.47879477 0.2009603094 0.092846463 0.39386860 -0.10064875 0.25767347 -0.006960737 -0.323002689 0.54088138 0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429 0.206128783 -0.38394575 -0.26111852 0.11124358 -0.307607156 -0.23108674 0.118623744 0.40568230 -0.35928390 -0.2287986403 0.0674126870 -0.194909729 0.406279736
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.19534471 -0.202157014 -0.31886736 0.257353003 0.09452472 -0.14337654 0.5803541 0.21971004 -0.48460389 -0.0910376333 0.143073239 -0.01343428 0.21924711 0.14911562 0.331156020 -0.623445470 0.26517213 0.10217269 -0.244826732 -0.08275136 -0.13342326 -0.18991201 0.2222643203 -0.008264954 -0.27726336 -0.32626055 0.55391119 -0.274223459 -0.41600613 -0.239476881 0.23644605 -0.33329094 -0.4140553740 0.3505474463 -0.034676768 -0.002314262
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.39571823 -0.352221233 -0.14016244 0.358512977 0.16414025 -0.26589439 0.6674822 0.17953342 -0.55049088 0.0562838685 0.021675321 0.57648156 0.11371008 0.29864451 0.104942610 -0.504014044 0.57693561 0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598 0.1109189257 0.023878095 -0.34214747 -0.25852067 0.28121726 -0.435798801 -0.31480707 -0.007553482 0.26670234 -0.45518879 -0.4532774636 0.2948129840 -0.267281290 0.463433745
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.30431379 -0.234295884 -0.27059673 -0.245346011 -0.06027442 0.04706860 0.3884300 -0.15945758 0.02075130 -0.0008356316 0.156613047 -0.06726357 -0.25892817 0.47051857 0.358948273 -0.512413738 0.41386623 0.25956799 0.146563139 -0.10384415 0.29375249 -0.32605966 -0.3406774353 -0.079363956 -0.25850079 -0.55407022 0.33385389 0.468934430 -0.03022371 0.104853773 0.29678304 -0.14204144 0.3091341703 -0.0449204187 -0.269151573 0.118249851
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.11231761 -0.062748045 -0.04494400 0.443120939 -0.43879510 -0.26298245 0.4742617 0.10248633 -0.35537405 0.1685276920 0.144103617 0.21438430 0.15584943 0.01726953 0.220675430 -0.319381715 0.48892920 0.46105569 -0.426727337 -0.19856115 -0.31952483 0.01320194 -0.0382402740 -0.043511121 -0.35219578 -0.12906627 0.26969235 -0.290367845 -0.32181822 -0.242589300 0.35793456 -0.18587339 -0.3767879009 0.3985766414 -0.191002663 0.343416703
KEGG_GALACTOSE_METABOLISM 0.06062020 -0.424855520 -0.03930301 0.349652791 -0.12188569 -0.46296074 0.5180153 -0.01789657 -0.35356594 0.2446797481 0.473003017 0.34499007 0.34112213 0.25024239 0.250381767 -0.453215048 0.57769569 0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855 0.056226416 -0.07839585 0.07879640 0.27290820 -0.414140702 -0.36050412 -0.191532611 0.39567826 -0.53298775 -0.4127888920 0.3440494486 -0.178365423 0.513262262
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.51820705 0.039968658 -0.12377878 -0.036122904 0.31985771 -0.46527398 0.3988617 0.01038232 0.37687330 0.5270758669 -0.001642410 -0.11679805 -0.05628187 0.71772103 0.241534280 -0.289882381 0.69553991 0.45968207 0.296411226 -0.50738472 -0.41554732 -0.27269571 -0.0503383811 0.414487589 -0.23400690 -0.52790283 -0.51602401 0.445718811 -0.42330633 0.174908837 -0.07311759 0.34397307 0.2085765041 -0.3221300091 -0.392502279 0.284751348
KEGG_FATTY_ACID_METABOLISM 0.20886138 -0.242876900 -0.30320811 0.187550569 0.29327773 -0.08700294 0.5230685 0.27380231 -0.34116554 0.1472345229 0.062594388 0.08687790 0.14291551 0.51283780 0.291434806 -0.504476008 0.43294161 0.28219716 -0.304791635 -0.30535668 -0.18442492 -0.13244662 0.0150691534 0.283488006 -0.48289609 -0.49976986 0.09652311 -0.011347711 -0.31278105 0.239631877 0.20679322 -0.03829960 -0.3295649579 -0.0001742616 -0.141024787 0.339491609
KEGG_STEROID_BIOSYNTHESIS 0.33604553 0.078851347 -0.52590310 -0.263728541 0.32226372 0.07485904 0.3016156 0.28921483 -0.28561530 -0.6241643849 -0.150031690 -0.31567564 0.10600143 0.12621865 0.040239055 -0.372783352 -0.17192551 -0.02763554 -0.362917924 -0.33311374 -0.30449600 -0.19719698 0.6253409182 -0.008988029 0.19293398 0.09900056 0.13681999 -0.119518167 -0.26419274 -0.013995204 0.20395478 0.11325134 0.1626070916 0.5348477961 0.511074525 -0.190211341
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 0.15739882 0.084600205 -0.52857163 0.553659439 0.26308379 -0.59676812 0.1225233 0.47452481 0.39641389 -0.4648496916 -0.432446416 0.25929223 0.48938377 -0.03614696 -0.087619025 -0.409483402 -0.39069390 0.44383724 -0.217291058 -0.06841149 -0.20808586 0.30133475 0.2338089031 0.628743013 -0.21619683 -0.24904089 -0.29348796 0.201532148 0.37954912 0.371373220 0.35506241 0.16613077 -0.1045489108 -0.3541049382 -0.187847376 0.005129543
KEGG_STEROID_HORMONE_BIOSYNTHESIS 0.38438742 0.113162544 -0.45530979 0.357007701 -0.25621878 -0.29318119 -0.1569740 0.14898979 0.39668852 -0.0468902937 -0.117557120 -0.02018489 0.05524139 0.23740098 -0.066581664 0.258410115 0.10847272 -0.13068365 -0.211051369 -0.28866137 -0.15360410 0.38750091 -0.3238802927 0.274917265 0.25281933 0.01163520 -0.01972985 0.521392285 0.25890358 -0.202780567 0.14930619 0.49695425 -0.0003891365 -0.4015589637 -0.319750989 0.216079876
KEGG_OXIDATIVE_PHOSPHORYLATION 0.03439798 -0.068230945 -0.24335287 0.179558503 -0.07748180 0.23899287 0.5355567 0.10928544 -0.58653812 -0.1232948723 0.011594465 0.25516015 0.10959538 0.23121819 0.196992997 -0.214021354 0.13140917 0.22589733 -0.167995266 -0.12327534 0.02643072 -0.11175039 0.0487111545 -0.293168402 -0.43460403 -0.36521148 0.06558919 -0.309035960 0.24113723 -0.186432466 0.25366326 -0.01546476 -0.1003451715 0.2488324612 -0.323304803 -0.197206582
KEGG_PURINE_METABOLISM 0.20191160 -0.108479208 -0.10596002 0.292297651 -0.05290036 -0.02776887 0.3629813 0.19221693 -0.19257184 -0.1570618328 0.049458419 0.10941378 -0.11575356 0.10624767 0.139611752 -0.104415107 0.24845743 0.18074380 0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986 0.14562604 -0.027395894 0.03493636 0.032161754 -0.01145234 0.00244119 -0.1717349277 0.1040248755 -0.158512548 -0.016876129
KEGG_PYRIMIDINE_METABOLISM 0.31268448 -0.315035601 0.02591551 0.453707816 -0.07827502 0.12111801 0.4400906 0.15739138 -0.34124605 -0.0079268025 0.045340682 0.11082758 -0.26167624 0.22159523 0.249023937 -0.267370796 0.21778307 0.26025801 -0.171924064 -0.24608881 -0.26204891 -0.28320893 -0.0131339608 -0.174961467 -0.39051601 -0.27174210 0.21371632 0.004495443 0.07795065 0.141105313 -0.08136747 0.09135035 -0.2760584617 0.3120288128 -0.422743981 0.010521260
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.04284560 0.242702474 -0.16024204 0.043647596 0.40725858 0.02861019 0.0869175 0.08096997 -0.05586613 -0.2040867733 -0.079009204 -0.30416447 -0.02979989 0.11484475 0.310350471 -0.167737512 0.02286110 0.02643017 0.079373530 -0.12361833 0.09011634 0.03828625 -0.2567878942 0.216249675 -0.26035482 -0.15309936 0.26950126 0.340594005 -0.28467469 0.223281462 -0.05508784 0.11421331 -0.0221915154 -0.3103008655 0.128094123 0.236156967
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.24472652 -0.281133287 -0.11156638 0.120281095 0.17443484 -0.21565939 -0.3081781 -0.11343483 0.31456894 -0.1543122886 -0.174461409 0.00981391 -0.39082192 0.15162090 0.304717020 -0.014069234 0.02620582 -0.23568881 0.193879486 -0.13962369 -0.14580659 0.28040853 -0.0968041965 0.295147940 0.20766864 -0.09101975 0.19914336 -0.142750362 -0.06039776 0.529969819 -0.28971540 -0.01846407 -0.0650840198 -0.3562492770 0.352102978 0.244584623
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.46919646 -0.380168943 -0.01773872 0.429812246 0.17364178 -0.20436261 0.3043864 0.34337161 -0.38080508 0.0857564710 -0.259409275 -0.05096080 -0.18249829 0.51288839 0.190289996 -0.436378420 0.26664702 -0.04414401 0.003940629 -0.49894385 -0.19574616 -0.05029689 -0.1798573066 -0.187265879 -0.11896302 -0.27828650 0.06494072 0.013637116 -0.27060418 0.395741143 -0.20169400 -0.05662690 -0.2624484362 0.0223987576 -0.151832657 0.296253623
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.13275992 -0.334172234 -0.25729613 0.213014739 0.16552566 -0.28549989 0.5557899 -0.12594035 -0.32547571 -0.0907632515 0.375179490 -0.05918342 0.18499723 0.52187226 0.300515960 -0.433259137 0.36300112 0.23581480 -0.253354935 -0.24446632 -0.23069885 -0.30728634 -0.1095251897 0.335974432 -0.42786720 -0.35467130 0.05607809 -0.014724657 -0.38384764 0.189365161 0.32880955 -0.10650837 -0.2283860731 -0.0006837462 -0.011463264 0.281658787
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.35031536 -0.131098230 -0.53101140 0.415024947 0.45022902 0.07344530 0.2667975 -0.21350030 -0.37419888 -0.6434244295 0.073570259 -0.16930988 -0.19093678 0.44377540 0.326753030 -0.395315587 0.20165887 -0.22843625 -0.345896575 0.21733136 -0.03379007 -0.33373706 -0.5598750406 0.105668958 -0.11338129 -0.25640184 0.53293944 -0.179140993 -0.15447191 0.309858597 0.28568125 -0.55068386 -0.2164372037 -0.1388932338 0.141542931 0.095210761
KEGG_LYSINE_DEGRADATION 0.18631105 -0.302707855 0.14202963 -0.001457447 0.05052599 0.13664666 0.3353993 0.17015808 -0.15999281 0.0003802554 0.054289069 -0.06841515 0.19332597 0.06780524 0.394846160 -0.308209809 0.06840594 -0.30368912 0.173959126 -0.20656156 -0.14215812 -0.10346628 0.1434771096 0.077612666 -0.18316752 -0.05935752 0.15458897 -0.072955358 -0.26549273 -0.117408842 0.01486245 -0.19612153 -0.3691316847 0.0986933555 0.018713137 0.172759177
KEGG_ARGININE_AND_PROLINE_METABOLISM 0.27398245 -0.007553433 -0.20383827 0.190912564 0.26352645 -0.08892086 0.3364975 0.08336217 -0.15782044 -0.0366667890 -0.011447268 -0.19979109 0.07225283 0.30484966 0.104227507 -0.292574794 0.28948741 0.07959214 0.004233241 -0.25695797 -0.29744163 0.17250236 -0.1975298264 0.243301838 -0.25109237 -0.11660031 0.11820678 0.051556447 -0.24134955 0.339674687 0.03932339 0.11905051 -0.1702678011 -0.1936881912 -0.061558207 0.052832710
KEGG_HISTIDINE_METABOLISM 0.32955287 -0.058544393 0.23401842 0.171291998 0.01579836 0.04289179 0.1478472 -0.19081266 0.10636274 0.0513523626 -0.227789459 -0.12657552 -0.23705948 0.17255355 0.063928642 -0.080957390 0.35225566 0.03053317 0.084445528 -0.09753282 -0.25255017 0.15575959 0.0462057297 0.127088199 -0.15801348 -0.39696091 -0.45105115 0.434357500 -0.03828497 0.050745235 -0.09141518 0.34481527 0.0778549056 0.1205808645 0.113071962 -0.107230492
KEGG_TYROSINE_METABOLISM -0.01013158 -0.196595442 -0.32598629 0.237374402 -0.23250901 0.20262459 0.2232565 0.26627457 -0.23842877 0.1924628476 -0.246173912 -0.11841733 -0.42705595 0.01951022 0.004484624 0.007798831 0.38715574 0.09743186 -0.182999776 0.20096611 0.40982753 0.05350491 -0.3214152163 0.182897748 -0.31135667 -0.45610097 0.33612797 0.127951123 0.29610319 -0.171090713 0.15670333 -0.08207433 0.2424991314 -0.0314562499 0.083631130 0.152278634
KEGG_PHENYLALANINE_METABOLISM 0.18148770 0.461371608 -0.62020227 -0.140393277 0.27692153 -0.20565575 -0.2649484 0.10789494 -0.12695163 -0.1941535369 -0.595583680 -0.09085442 -0.46311485 -0.44379258 -0.093990808 0.280938193 0.09934493 -0.08162794 0.486358071 -0.06639144 0.37934632 0.56113507 -0.1060230711 0.468069197 -0.17744056 -0.17662290 0.14870307 0.649119193 0.19443272 -0.290354517 -0.55479111 0.45091097 0.3370977631 0.1944685634 -0.125721282 -0.096339449
KEGG_TRYPTOPHAN_METABOLISM 0.02655589 0.043109593 -0.31856690 0.098466690 0.13008831 -0.18630463 0.2146807 0.05227151 0.09215733 -0.1502355445 0.007752516 0.06575941 0.14715900 0.31087022 0.208518310 -0.129119060 0.15933118 -0.11659123 0.158404342 -0.40413725 -0.29996492 0.20866768 -0.0003029911 0.127581506 -0.15098840 -0.26429807 -0.09215367 0.330810321 -0.29378958 0.015665134 -0.06172804 0.33048668 0.0406671480 -0.0549421996 -0.009869338 -0.070819327
>
> gbmPar <- gsvaParam(gbm_eset, brainTxDbSets, maxDiff=FALSE)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up -0.3047539 -0.2946860 -0.1834593 -0.5442776 -0.2834175 -0.2788147 -0.3003514 -0.2874994 0.2607199 0.1413387 0.2146940 -0.3180027 -0.4002297 0.1769516 -0.2588480 -0.3482341 -0.2662723 -0.3459269 -0.4173384 -0.1983332 -0.1586231 -0.3486947 -0.3458663 -0.2206452 0.2825297 -0.3877544 0.2093004 -0.2012996 -0.3454799 0.1747717 -0.1457140 0.1895460 -0.2553038 -0.3954264 -0.1289837 -0.3769329 -0.4737155 -0.3632470 -0.3043683 0.2444025 -0.3233087 -0.4249789 -0.3426041 -0.2380239 -0.3075525 -0.3459151 -0.3087816 0.2381330 -0.2643738 -0.2797349
astroglia_up -0.5149583 -0.5410770 -0.4707559 -0.6113382 -0.4302575 -0.3653708 -0.4790737 -0.4724831 0.2019720 -0.5165498 -0.3810421 -0.4003590 -0.3525063 -0.4778482 0.1594521 -0.2744265 -0.4668132 -0.5181954 -0.4725050 0.3496106 0.1632234 -0.5350220 -0.5062797 -0.5565810 -0.2063866 -0.4462150 -0.1671050 -0.4503466 -0.5630672 -0.4053433 0.1609667 -0.1794776 -0.4755774 -0.2128034 -0.1997192 -0.5332830 -0.4417129 -0.4310179 -0.4982304 0.2722387 -0.3527572 -0.4120461 -0.5092322 0.1534758 -0.3638957 -0.2886322 -0.3058095 -0.2268245 -0.3789481 -0.4199315
neuronal_up 0.5535049 0.2417091 -0.2419423 -0.1264513 0.5321516 -0.1907802 -0.3594715 0.3119123 0.4301345 -0.1251531 0.6345184 -0.4761376 -0.4777196 -0.3691534 0.2468458 -0.3802419 0.4236358 -0.4473820 -0.1168248 0.2615203 0.4412960 0.2258959 0.4605784 -0.1201504 -0.2601714 -0.2213066 0.5831010 -0.3449359 -0.3518502 0.1186366 0.1916525 -0.3076000 0.3498210 0.4973920 0.6397865 -0.2787217 0.2572456 0.4607110 0.3686673 0.1846618 0.5245801 -0.3509494 0.3513964 0.5454430 0.1606448 -0.2953076 -0.5303268 0.6995543 0.1475983 -0.1844540
oligodendrocytic_up 0.3317492 0.2491713 0.3353197 0.1965032 0.4766178 0.3696743 0.1739008 0.2837137 0.3965796 -0.2499617 0.4111354 0.3145638 0.6296969 0.3363415 -0.1374640 0.4114245 -0.3041959 0.2647537 0.4139883 0.2318300 0.3873472 0.2032636 0.4537419 0.2660245 0.5308132 0.4464649 0.5707848 0.3329401 0.4571077 0.2958584 0.3318632 0.4968947 0.3523085 0.5364637 0.4087340 0.5468353 -0.1492890 0.4105960 0.5855587 -0.1819342 0.4798445 -0.1856330 -0.1874635 0.4959465 0.5271533 0.2206708 0.2340045 0.2860177 0.1995836 0.1418165
TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up -0.4388712 -0.2984390 -0.2418500 0.2967027 0.2963262 0.5497730 0.2387450 0.3144786 0.3333460 0.2297994 0.2686543 0.2357884 0.3223822 0.2434233 0.4129700 0.3558037 0.2586949 0.2957692 -0.1293295 0.4002767 0.2431737 0.2064763 -0.2054680 0.2098025 0.2378884 0.1979041 0.2823311 0.1955658 0.3445508 0.2594091 0.2529872 0.4826020 0.1815513 0.4318795 0.2885936 0.3123410 -0.3779783 0.1939708 0.1641413 0.1497425 0.2281183 0.1198567 0.3737903 0.2232357 0.2131509 0.2635626 0.2295927 0.2025863 0.3654367 0.3070467
astroglia_up -0.5577897 -0.3009622 -0.4952939 0.3562099 -0.1948617 0.2506709 -0.1956322 0.2980680 0.1473354 0.1866536 -0.4623550 -0.1714237 -0.4221490 -0.1818365 -0.2457673 0.2500337 -0.2661463 -0.1506672 -0.4899183 -0.3467717 0.2013752 -0.1561121 -0.2157769 -0.2982904 -0.3172812 -0.2281312 0.2970433 -0.2815591 0.1634429 -0.1746780 -0.3294734 -0.2707020 -0.3002505 0.3839744 0.2305549 -0.1605050 -0.2294543 0.4619706 -0.1943197 -0.2982120 -0.2123044 0.3634887 0.2863492 0.3384878 0.1948430 0.1395315 -0.2248029 -0.2162429 -0.2067516 -0.3013420
neuronal_up 0.2111547 0.1714030 0.4657383 0.5497687 -0.3946098 0.4963120 0.3352992 0.7175166 0.4972767 0.3710156 0.7631191 0.5344811 0.7969773 0.2856497 0.3129090 0.6442165 -0.2297751 0.4688783 0.7186127 0.1864052 0.1512623 0.4905083 0.5779253 -0.1747120 0.7386962 0.5896950 0.2983598 0.4279023 0.2145936 0.1761452 -0.5754318 0.4795529 -0.6007193 0.6585229 0.2712467 -0.5609244 -0.5409766 -0.5582310 -0.1397818 -0.1699394 0.1369626 -0.2852583 -0.2074379 -0.3609699 -0.4746596 0.2723624 -0.1921239 -0.6249382 -0.1989687 0.4172576
oligodendrocytic_up 0.3666431 0.3008428 0.3834914 -0.2197493 -0.4632601 0.1755629 0.2283133 0.3855686 -0.1581432 0.2212679 0.2711446 -0.1950745 0.2557408 0.2960432 -0.1573391 0.3797065 -0.3338795 -0.2831008 -0.2227159 -0.1671839 0.4939055 0.1723784 -0.2516605 -0.1981382 0.3178961 -0.3937384 -0.2466558 -0.4638286 -0.4636637 -0.2714250 -0.3701235 0.2071280 -0.3779293 -0.3386804 0.2197589 0.2601284 -0.3611962 0.1908298 -0.4231171 -0.3430255 -0.3512123 -0.2820085 -0.3780724 -0.3704518 -0.3216412 -0.3171512 -0.2142009 -0.2771720 -0.1908734 -0.1300848
TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up 0.4009205 0.3415409 0.2219087 0.2208367 0.2603907 -0.1765010 0.2940235 0.2124375 0.4061779 0.4328053 0.2173015 0.3551808 0.2219615 0.4042258 0.3642527 0.3044645 0.3551091 0.4812290 -0.2947330 0.2717050 -0.2072296 -0.2471975 -0.2842497 0.3991259 -0.2766075 -0.1677575 -0.2641184 -0.1595722 0.1984901 -0.2226697 0.1713801 -0.2188904 -0.2579632 0.1518073 0.1637208 0.3756718 0.2550845 0.1295303 -0.2700193 0.2063444 0.1624008 -0.3704812 -0.2729261 0.1962416 -0.1590410 0.3119768 0.2627011 0.2888753 0.2002931 -0.1400612
astroglia_up -0.2684818 -0.2478927 0.4042948 0.2335354 -0.4561683 -0.2852517 0.2751976 0.3726306 0.3118150 -0.2394383 0.1820660 -0.2988110 0.1652119 0.1841336 0.2581383 0.2056429 -0.2597831 0.3690882 0.4820315 0.2887467 0.5403445 0.4579650 0.5444281 0.5331769 0.3394440 0.2194871 0.5238034 0.4465451 0.4552118 0.3171873 0.5092584 0.4264341 0.3355302 0.4395682 0.3572217 0.5354133 0.5529363 0.3635790 0.4608111 0.3641927 0.4291813 0.4496740 0.4566347 0.3510896 0.4412179 0.3601076 0.3276640 0.5528990 0.4514321 0.2932687
neuronal_up 0.4714021 -0.5453959 -0.2184275 -0.6205832 0.3765956 -0.4810052 -0.3898214 -0.3376351 0.4026263 0.2958724 0.1514880 -0.5448607 0.4816556 -0.5156220 -0.5857302 -0.3912544 -0.4810045 -0.4432014 -0.3401462 -0.2069768 -0.1755817 -0.5429475 -0.3473447 0.4293285 -0.1852551 -0.2807897 0.2095081 0.1692813 -0.5953110 -0.4569613 0.4986510 0.6780347 -0.4361162 -0.2657947 -0.4149003 -0.2019748 -0.1825776 0.4705841 -0.3660470 -0.3950770 -0.2875748 -0.3687514 -0.4339034 -0.4137328 -0.4061838 -0.3665761 -0.2886278 -0.4494102 -0.4614783 0.3012511
oligodendrocytic_up -0.2170210 -0.3505377 -0.4033821 -0.4180423 -0.4282208 -0.4921075 -0.3129745 -0.2568446 -0.4508574 -0.3521717 -0.1932037 -0.2401757 -0.4705363 -0.4756500 -0.3939968 -0.4508653 -0.4673510 0.6267838 -0.3869379 -0.1753464 0.1398180 -0.3356724 0.2174792 -0.1909474 -0.4170448 -0.3449788 -0.3789635 -0.3723979 -0.2489271 -0.2955629 0.2563263 0.5062260 -0.3722382 -0.2544347 -0.4120718 0.1481816 0.2266027 0.2624142 0.6390087 0.1041047 -0.3246204 -0.2504649 0.1695500 0.3362893 0.2602318 -0.4512150 -0.2275365 -0.4490874 0.2728064 0.1801245
TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up -0.3141722 0.2699874 0.2219473 0.2091188 0.2345999 -0.2194917 -0.3453076 -0.4238358 0.3549822 0.2340566 -0.2593196 0.1099604 -0.2273672 0.2019316 -0.2041700 -0.1508235 -0.2519564 0.1867464 -0.1965190 0.2585439 -0.3990271 -0.3061357 0.1651281
astroglia_up 0.3922137 0.2846455 0.4656351 0.5682138 0.4886159 0.3895400 0.3730679 0.2343013 0.4820948 0.3943550 0.4396104 0.5514612 0.4772503 0.5054087 0.5478562 0.3711037 0.3050986 0.2872253 0.2808018 0.5497252 0.4051805 0.4516472 0.4085658
neuronal_up -0.4367833 -0.3295978 -0.2846818 -0.4517050 -0.3885191 -0.3608320 -0.3779686 -0.3484378 -0.2868552 -0.5719856 -0.2625708 0.2935293 -0.3335214 0.6340333 -0.4788773 0.5079833 0.1255322 0.2449831 -0.5029271 -0.3891953 -0.3632664 -0.4659142 -0.2670667
oligodendrocytic_up -0.1680797 0.2981662 -0.4332569 -0.2097164 -0.4411032 -0.4515751 -0.1344606 -0.2894701 -0.3966829 -0.3681011 -0.2038674 -0.1537039 0.2336640 -0.2932406 -0.2495044 0.2091980 -0.3179201 -0.3245650 -0.2703005 -0.4534530 -0.4265475 -0.4192150 0.1600080
>
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> leukPar <- gsvaParam(leukemia_eset, cgpC2BroadSets,
+ minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP -0.284185921 0.09894281 -0.09166085 0.15556858 0.018687701 0.21589856 -0.159760678 -0.39128861 -0.26727234 -0.44679630 0.325744327 -0.23951518 0.051302632 -0.278506974 0.04015073 0.347632324 -0.24804097 -0.38938143 -0.15524618 0.19043913 0.02370623 0.068903997 -0.29422954 0.36158458 0.322237127 -0.075044727 0.18750433 0.22546588 -0.150244738 -0.132861970 0.245771407 0.253424577 0.149179429 0.256834003 0.54585089 -0.13771429 -0.381283518
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP 0.074234671 0.28539841 0.54867983 -0.21455850 -0.196029929 -0.25981972 0.473892865 0.08132092 -0.02781303 0.54530761 0.366563615 0.32206336 -0.020333305 -0.304173959 0.16484183 0.025761275 0.04010094 0.12058207 -0.28234199 -0.32765526 0.33755016 0.062136062 -0.17438543 -0.27714732 -0.175368929 -0.068632830 -0.16029136 -0.54312340 -0.457243901 0.063838909 0.284048174 0.451910696 0.065458637 -0.216675403 -0.09964422 -0.46293573 -0.471055266
WINTER_HYPOXIA_UP -0.122226539 0.19658831 0.19027777 -0.19779261 -0.295049369 -0.24808384 -0.216814893 -0.14968164 -0.14439647 0.16117004 -0.263075768 0.24300974 0.212753169 0.219567220 -0.26389007 0.067029667 -0.06856209 -0.08909042 -0.05226506 -0.30733660 0.22533379 0.193092854 0.04216994 -0.27030754 0.146503383 0.248352494 -0.08507045 0.02799035 -0.019718990 0.163757054 0.226094520 0.147465095 0.144632935 -0.177600100 -0.03490205 -0.02579216 -0.201473546
PYEON_HPV_POSITIVE_TUMORS_UP 0.373338180 -0.08195895 0.49691537 -0.35523689 0.073820829 0.08656391 0.257900378 0.52264452 0.40765416 0.46023184 0.085547216 0.57035112 -0.453573874 0.127033813 0.41338035 -0.144148442 0.34650611 0.42161444 0.05076537 -0.50755967 0.06858839 -0.122209941 0.14630225 -0.46393255 -0.297018214 -0.007595085 -0.17430019 -0.34867040 0.238611621 -0.485707594 -0.393180984 0.283583934 -0.117141935 -0.264746769 -0.50063635 -0.42226439 0.030286161
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP 0.034852372 0.17810998 0.33466738 -0.18043537 -0.301630159 -0.25696203 0.069464046 -0.13728252 0.03289923 0.15662255 0.008254385 0.17876533 -0.035728864 0.263860776 0.18841806 0.054449457 -0.05893731 -0.03627519 -0.02106037 -0.30409556 0.26346145 -0.033555920 -0.09904109 -0.31073293 0.196059298 0.041943377 -0.27670124 0.05374531 0.102078549 0.089751050 0.126164281 0.073107504 0.159604038 0.149992036 -0.17339221 -0.12806055 -0.183128694
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP -0.297408395 0.12039801 -0.26428063 0.17004586 -0.039805152 0.09850287 -0.057298350 -0.35386190 -0.16713553 -0.07892505 0.200098274 -0.20933571 0.144977450 -0.026805809 0.09893933 -0.004404619 -0.15285474 -0.30327609 -0.06851817 0.09694832 -0.24544948 0.118722964 -0.34259752 0.15768732 0.172784905 -0.184720574 0.19647116 0.20367723 -0.143437960 0.203937367 0.294431435 0.184358331 0.272106482 0.260812933 0.29031258 0.18633750 -0.058307777
LU_TUMOR_VASCULATURE_UP -0.303485092 0.05954910 -0.08947968 0.17393748 0.055216604 -0.21711694 -0.068811743 -0.36596763 -0.10701941 -0.26356696 0.360410658 -0.07864957 -0.121613155 0.177822010 -0.01104916 0.229093881 -0.18613941 -0.27316309 0.12995187 0.27171808 -0.30894560 0.172438331 -0.30343314 0.37190436 0.180795286 -0.104016386 -0.07390340 0.21484484 -0.372653361 0.272063159 0.146426458 0.292726824 0.073215278 0.236064108 0.12233488 0.30677400 -0.166297976
KORKOLA_EMBRYONAL_CARCINOMA_UP -0.237891606 0.22324873 0.36244453 -0.10961418 -0.136474592 -0.46990350 -0.273764475 -0.16989735 -0.22372057 0.11247316 -0.232337649 0.28697934 0.017986838 0.142356962 -0.07127081 0.189358376 0.18951708 0.36031203 -0.18122486 -0.25323494 0.42996355 0.240702262 0.14655134 -0.29879857 -0.105909705 -0.186176950 -0.23520759 0.11808592 0.123806950 -0.096186587 0.082449346 0.068290275 0.204362056 -0.305158509 -0.18242290 0.07924085 0.050412994
KORKOLA_TERATOMA_UP 0.069466630 0.31282751 0.26793152 0.09145777 0.364378105 -0.01610294 -0.429410344 -0.34268743 -0.49321544 -0.29390567 -0.294556431 -0.43171623 -0.275085564 -0.198360712 0.34983219 0.320807082 0.13961117 -0.13440310 0.10165153 0.12248119 0.32044205 0.106653855 0.01837852 0.25031318 -0.310896163 0.053773795 0.03604947 0.33071217 0.066562201 0.280163027 0.039476681 -0.126383734 0.241910733 -0.323470237 -0.03914776 0.30954031 0.103077314
KORKOLA_YOLK_SAC_TUMOR_UP 0.165072940 0.38624888 0.50530097 -0.37418563 0.006252226 -0.41666427 -0.301013273 -0.13354266 -0.14397323 0.31804861 -0.080548556 0.23290348 0.035345111 0.007931487 -0.09467101 -0.158566311 0.29400647 0.34421179 -0.14156018 -0.16187218 0.22342054 0.257582308 -0.07203685 -0.28296980 -0.390797184 -0.299345198 -0.33442798 -0.05640545 -0.267890012 -0.360997781 0.046532067 -0.038161214 0.260330724 -0.286721001 -0.29560478 0.25567578 -0.058961842
KORKOLA_CHORIOCARCINOMA_UP -0.010233903 0.32695285 0.23409239 -0.44995947 0.110491619 -0.77486388 -0.590305245 -0.30294240 -0.37350003 0.22506301 -0.122120864 0.36713585 0.321071992 -0.025352644 0.18055781 0.006019335 0.33689753 0.01559227 -0.39322807 -0.49057169 0.60777944 0.563917133 0.23716208 -0.44914903 -0.257199360 0.181773354 -0.26429369 0.34875870 -0.418331961 -0.402954949 0.279270709 -0.219024970 -0.073131401 -0.377126885 -0.01449304 0.08204518 0.009841082
KORKOLA_SEMINOMA_UP -0.298212257 0.01080115 0.24405821 -0.15938874 -0.027952932 -0.28780633 -0.247319424 -0.33519149 0.06014085 0.22168793 0.058430886 0.28316538 -0.005576346 0.060208089 0.07375198 -0.081445539 0.16610491 0.42430320 -0.01533883 0.08230093 0.24992576 0.077656272 -0.06562014 -0.16684190 -0.284188016 -0.287282092 -0.16462701 -0.05811647 -0.062401658 -0.099243073 0.073201955 0.067154795 0.267030362 -0.298357838 0.02900301 0.32555350 0.080225727
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP 0.097593813 -0.16794685 0.35151193 -0.23237964 -0.163197206 -0.29950843 -0.006714904 0.34062208 0.09604888 -0.11003744 -0.171064434 0.06587775 -0.266062516 0.220122655 0.33608928 -0.127916894 0.11383392 0.19988434 0.20190981 -0.30021326 0.14299295 0.063923084 0.05677644 -0.28986580 0.038510117 -0.159509213 -0.29388778 0.05765373 0.326704138 0.074522409 -0.274247777 -0.275056415 0.053402889 -0.002107284 -0.34859857 0.03644107 0.208732689
HOLLMAN_APOPTOSIS_VIA_CD40_UP 0.105496299 -0.13988837 0.38579893 -0.24564927 -0.083118397 -0.02283095 0.141139992 0.25611563 -0.05713898 0.01803229 -0.087474542 0.14542629 -0.210191344 0.211687858 0.22093653 -0.133326040 0.06549381 0.18478682 -0.03775017 -0.20148605 0.22321211 -0.059252095 0.01426428 -0.09291203 -0.005412103 -0.025056156 -0.28678304 -0.10392565 0.206300949 0.073580108 -0.204915942 -0.221567934 -0.045463659 0.033396194 -0.24875118 0.01892772 0.157710229
LIU_PROSTATE_CANCER_UP -0.224388256 0.06307335 -0.08241727 -0.04832687 0.189906903 -0.02124567 -0.279030644 -0.27886322 -0.09392327 -0.19792744 -0.029580432 -0.03027978 0.202657103 -0.340883536 -0.03209933 -0.116168855 -0.30287655 0.21450416 -0.04221989 -0.04528200 0.06964423 0.083598831 0.16642355 0.12185052 -0.000928352 0.140595272 0.28592176 0.02379778 -0.071982214 0.154329444 0.077278879 0.239783535 0.316168936 0.045907958 0.11350734 0.06778064 -0.142535169
LIU_SOX4_TARGETS_UP 0.121044935 -0.14068822 0.22940559 -0.01597795 0.061591507 -0.00693642 0.014199778 0.30911203 -0.08600822 -0.02038572 0.114287917 -0.21978031 -0.226307014 -0.023607467 0.29166627 0.064022632 0.06822989 -0.07130524 0.23335358 0.06981417 -0.11573705 -0.291602661 -0.13629614 -0.03270145 0.024218801 -0.013336764 -0.10693992 -0.16558042 0.190828338 0.225771717 -0.229823064 -0.164944356 -0.179080910 0.177092706 -0.17646028 -0.18791880 0.240962021
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP 0.062841657 -0.18362789 0.29336781 -0.18594491 0.154299300 -0.05557008 -0.083102532 0.04576576 -0.09217560 -0.19543518 0.055196463 -0.04809592 -0.052719541 0.107250567 0.17234102 0.220352187 -0.04953385 0.24873127 0.13828440 0.19314948 0.04975678 0.049538498 -0.06477196 -0.06226135 -0.098276136 -0.129915554 -0.19707557 0.02496088 -0.051271962 0.052870430 -0.073226448 -0.184972633 -0.012686096 -0.071808834 -0.27150226 0.27912570 -0.135303937
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP -0.094846112 -0.07207493 -0.02804641 0.03696695 -0.086436392 -0.08397341 -0.068172639 -0.05763452 -0.02656466 -0.17775526 0.258308865 -0.14822566 -0.145150486 -0.039994112 0.10916677 -0.090893212 0.03680901 -0.09371656 0.11806513 0.17785724 -0.11045327 -0.058180594 -0.31826977 0.09626481 0.143735941 -0.160260444 -0.06107374 0.08258827 0.034945942 0.261716811 0.008073164 -0.089058343 0.056294586 0.251527056 0.01348282 0.28709952 0.102083930
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP 0.074340051 0.02857125 -0.24003150 0.30715667 -0.010403308 -0.10045962 -0.159844495 -0.22324560 0.02880624 0.11715699 0.077777052 -0.17990167 0.106011986 -0.179976522 -0.09660455 0.026469354 -0.12555729 -0.17002077 0.19363609 0.07413777 -0.34472957 0.071120620 -0.23684660 0.25225819 0.214521242 -0.165874245 -0.03452474 -0.02439650 -0.180590309 0.011098030 0.114305528 0.052961087 -0.068405608 0.293293442 0.24643595 0.09297256 -0.030979738
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP 0.005014724 0.08111308 0.26913235 -0.09552045 -0.450228901 -0.20835559 -0.341832089 0.08934729 -0.33423215 -0.07570491 -0.227456658 -0.31425832 -0.075046342 0.101225498 -0.22803411 0.359148102 0.25779762 -0.50524646 0.12655983 -0.08326589 0.16277302 -0.238058161 -0.17065282 0.06861909 0.125783171 -0.153453577 -0.06888951 0.35891268 0.238976848 0.449575492 -0.397721447 0.129949315 0.063354595 0.344276854 0.21919705 -0.02084416 0.446602851
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP -0.086490808 0.42662285 -0.06186335 0.19254225 -0.147417154 0.23175825 0.491914629 -0.11696009 0.01145265 -0.18617542 -0.098643515 -0.08071038 -0.040838732 -0.284554435 0.44402053 -0.167965862 -0.06796364 -0.12183172 0.37256760 0.34632681 0.01477953 0.154501865 -0.14155636 -0.17148626 0.040841265 -0.199318164 -0.03141871 -0.02556187 -0.194745034 0.111576773 0.299019277 -0.246935585 -0.304924920 0.249744542 0.16874813 -0.28320150 -0.409684665
FRASOR_TAMOXIFEN_RESPONSE_UP 0.095102205 0.13613061 0.27963248 0.10696680 -0.201251938 0.04440738 0.039666191 0.08072985 -0.30347286 -0.13117213 -0.163829152 -0.08811162 0.130289925 -0.269491251 0.04481561 -0.129982372 -0.09261704 0.05779261 0.20931794 -0.11293941 -0.08782228 -0.154603301 -0.10942582 0.03255269 0.068908002 -0.134879788 -0.11865894 0.03929191 0.105215621 0.144775760 -0.132818191 -0.126161041 0.046198277 0.066790819 0.10784581 0.14897625 0.103889267
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP -0.093263740 0.24451532 -0.30875436 -0.01171828 -0.077592391 0.06977365 -0.047698353 -0.25543630 -0.16734657 -0.29943342 0.138659259 -0.24677548 0.008316094 -0.097198227 -0.07991562 0.237943766 -0.08176618 -0.34607119 0.18984664 0.28121888 -0.29765020 0.006609358 -0.17838613 0.18555511 0.093828022 -0.218609231 0.17434097 0.06804717 -0.095062879 0.199580074 0.321860622 -0.008284166 -0.001916854 0.183088620 0.25305607 0.13585610 0.034581179
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP 0.203957767 0.12189117 0.38492132 -0.24300464 -0.090523098 -0.19966713 0.102728363 0.04976671 0.18283638 0.30437400 0.148109727 0.24724848 -0.327248458 0.129670458 0.33143975 -0.086102559 0.10335793 0.20068518 0.03773511 -0.23454620 0.13617294 -0.090673447 -0.26073243 -0.38875239 -0.054723088 -0.050551494 -0.23180710 -0.12601589 -0.001883262 -0.007476349 0.072573918 0.189048383 0.090254301 0.187420576 -0.31338258 -0.10912037 -0.247410905
WATANABE_COLON_CANCER_MSI_VS_MSS_UP -0.156524705 -0.00167507 -0.10689295 0.36427412 -0.010218876 -0.06496857 -0.269749963 -0.27745767 0.02119152 -0.21830558 -0.196574719 -0.35120814 0.269162954 -0.142483756 -0.26808257 0.038724466 -0.07004319 -0.11588327 -0.10292213 -0.06427425 0.25284346 0.283925446 0.01040659 0.32549432 0.230151042 0.409316724 0.37175290 -0.27673142 -0.066751401 -0.078279396 0.099369827 -0.165196141 0.013360644 0.168730310 0.23632001 -0.18337713 -0.329485400
>
GSVA.Rcheck/tests/test_plage_newapi.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> ## 2023-11-10 axel: simple test script for method PLAGE, new API
>
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db
> library(GSVA)
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 1.4171739 -1.3444519 -0.99052898 0.4203395 1.30716224
g2 -0.7281951 0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754 0.09779699 -0.6792548 -0.09124045
g4 1.0735382 1.3156255 0.15588330 -1.8079608 0.48531108
g5 0.7229884 -0.9162342 1.93982245 0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> plagePar <- plageParam(X, gs)
> plage.es <- gsva(plagePar, verbose=FALSE)
> dim(plage.es)
[1] 100 30
> plage.es[seq.int(min(nRowsToPrint, nrow(plage.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 -0.029219588 0.134185958 0.3713074711 0.0407816079 0.06092767 -0.220481051 -0.263761945 0.150320487 -0.22409656 0.009584613 -0.39111762 -0.1302648585 -0.05959038 0.33696215 -0.07282788 0.073310843 0.05147115 -0.2483084427 -0.0858324287 0.178309261 0.38540679 0.046642663 0.122541902 0.015905580 -0.097924551 0.029203351 -0.06630956 -0.07126728 -0.194205126 0.14834577
gs2 0.009713309 -0.070894760 0.0887748898 0.0438945086 0.07597568 -0.099232840 0.257432656 -0.180783042 -0.26082831 -0.191077787 0.03035706 -0.1035337259 -0.19412605 -0.10714563 0.07146483 0.086637398 0.20308822 0.0140285507 -0.2137568863 0.239387383 -0.22371195 -0.206819710 -0.133382606 0.108114986 -0.046079067 0.089875594 0.42299690 0.41937892 0.096947556 -0.22669608
gs3 -0.139922266 -0.117741577 -0.0781834024 -0.2165908186 0.27378251 0.311048702 0.086846172 0.044475856 -0.08203218 0.119527132 0.03846745 -0.2109524281 0.12655940 -0.38507377 0.10369939 -0.017494211 0.16994906 -0.1420728947 -0.0785235706 0.004983979 -0.08761015 0.009889028 -0.094132008 -0.247835746 0.083711263 -0.250047995 -0.11800166 0.26164152 0.264615361 0.36701785
gs4 0.136784356 -0.055804012 -0.0003340026 -0.1516269802 -0.27114196 -0.083083560 -0.096565517 0.036868895 -0.06300502 -0.221561203 -0.19813522 0.1042473505 0.08093850 0.05674063 -0.19895817 0.067302708 0.25451893 -0.0005207089 -0.1159880895 0.048467793 -0.20603836 0.159545022 0.044036214 0.534771648 0.105886354 -0.017032347 0.07891909 -0.39111885 0.312125306 0.04976120
gs5 0.034934164 0.039749845 0.1228855856 -0.2732261283 0.04199286 0.103214014 -0.195436449 -0.287379571 0.03966687 0.303622722 0.07474143 0.0856083346 0.13595773 -0.01383837 0.35831980 -0.051209828 -0.43727399 0.1718981370 -0.1181945240 0.089941405 0.27917773 0.023292236 0.118740362 -0.297527028 -0.070561479 -0.048431187 0.02429263 -0.23305662 0.114527349 -0.13642802
gs6 -0.279844320 0.191897986 -0.3053996126 0.0094415284 0.04842640 0.194020478 0.096966418 -0.068898812 -0.20073135 0.378243740 -0.19309702 -0.1466213408 -0.14129713 -0.26167877 0.16969940 0.003873402 -0.06359659 0.1923023239 -0.2857295678 -0.037571361 -0.13741602 0.028278539 0.238658744 -0.074846882 0.198735207 0.142033651 0.30737897 -0.09691484 0.003752428 0.08993441
gs7 0.225539026 0.254315627 0.0211474628 0.3655580391 0.12888554 0.040475802 -0.108671963 -0.177723642 0.41116878 0.227671549 -0.28572797 -0.0471024585 -0.11298848 -0.14563561 -0.04101156 0.001529252 -0.30955146 0.2015628322 -0.0515248852 -0.202779772 0.26345240 -0.037525716 -0.006683093 0.089664221 -0.112755956 -0.152690537 -0.11819571 -0.06373540 -0.095213785 -0.16145252
gs8 -0.231283677 -0.053675557 0.0264131810 0.1359540470 0.08233788 -0.227928562 -0.087182432 -0.090687865 -0.08943693 0.307308887 -0.26623882 0.0138228392 0.21217554 -0.01320852 -0.37951349 -0.052096781 0.10783552 0.1598299126 -0.2189896514 -0.112309675 0.24977969 -0.065970466 0.140396761 0.076196677 -0.330320943 0.135782120 0.26952133 0.29550850 -0.055760954 0.06174143
gs9 -0.149696707 0.070112664 -0.3927757978 0.0404540759 0.05022070 0.286507502 -0.292734447 -0.111830390 0.01797344 -0.123194982 -0.12329977 -0.0405767884 0.05003308 0.38368419 0.01421485 0.062677869 -0.07909931 0.0486677864 0.0095880253 0.132223596 -0.28737944 0.178169340 -0.379773116 0.242912453 0.188194766 0.217203390 0.11001738 -0.02903181 -0.001529958 -0.09193259
gs10 -0.117672007 0.025542827 0.1308302520 -0.1626636222 -0.09699436 0.244461645 0.359249078 -0.191834856 0.03983472 0.146795086 0.06267437 -0.0434347372 -0.04176742 -0.06732570 0.13904093 -0.305077580 -0.02187673 0.1570480436 0.1334628532 -0.279021420 0.06938138 0.363531649 -0.201888466 0.258009015 0.084167939 -0.202884988 0.12079417 -0.11859744 -0.252643549 -0.23114107
gs11 -0.117405216 -0.048550062 -0.2152359244 0.1765495035 -0.15055137 -0.123720213 0.102298045 -0.027754231 0.20009873 0.250537460 -0.05653296 0.5188172981 -0.14533038 0.18956907 -0.05111332 -0.028603358 -0.08113559 -0.1326973408 -0.2163548884 0.153306782 -0.24927555 0.377259651 -0.143092985 -0.138807673 -0.201352437 -0.049677679 -0.09122352 0.11203847 0.069118818 0.11882086
gs12 -0.543671749 -0.184614928 0.1099977497 -0.0553393639 -0.40340420 0.033822756 0.082140727 0.090566044 0.06267315 -0.035981570 0.18191246 -0.1165185323 -0.14432586 0.18146646 0.03547440 0.236193030 0.02238259 0.0383756956 -0.0935119488 0.043760861 0.02041612 0.063399434 0.120073412 0.080158878 -0.122419354 0.011193111 0.21268970 -0.20265505 -0.123185463 0.39893143
gs13 -0.024887916 0.118584422 0.1388041889 -0.1413124768 -0.39825505 0.052045207 0.261267389 -0.255779352 0.08983137 0.244926313 0.25970077 -0.0188348892 -0.36760612 -0.01271960 -0.20002981 -0.087057056 -0.05944590 -0.1591285151 0.2077404356 0.302011283 -0.02371886 0.178685780 0.016103242 -0.065410956 0.141870716 -0.181431006 0.21774895 -0.11979818 0.016494216 -0.13039859
gs14 -0.100340055 0.077189402 0.0390858762 -0.0370017538 -0.38389060 0.184412799 -0.118805404 0.151984291 -0.25219352 -0.107177720 -0.13513101 0.0625168832 -0.10590181 -0.17815359 0.03224044 0.159411109 -0.08896745 -0.1280661493 0.1577303651 -0.038406698 -0.27702921 -0.122279723 0.239019808 0.128024840 0.212749941 0.142712690 0.18985273 -0.29773955 0.378010038 0.21614304
gs15 0.048774560 0.060119682 0.0484913743 0.2519843778 0.03039694 -0.234375681 -0.108291508 -0.453456336 0.06303550 0.086507823 -0.04349266 0.0260079589 -0.07031311 -0.07260948 0.19503960 0.264057607 0.30593891 0.1027550963 0.2715334959 -0.065807601 -0.15451764 0.253065015 -0.142033610 0.149114814 -0.156868088 -0.142545833 -0.28141243 -0.15529889 0.134277793 -0.21007769
gs16 -0.121838108 0.078038618 0.1774058118 0.3701311334 -0.27325953 0.179212470 -0.183228978 -0.297884469 0.07431105 0.142904264 -0.37912167 0.0392912596 0.31140398 -0.15567324 0.30015891 -0.075661103 -0.09261959 0.0039456916 -0.0540112724 -0.046884108 0.18371220 -0.073575237 0.236113549 0.114082325 -0.059486224 -0.043877650 0.05583114 -0.19847973 -0.131850692 -0.07909080
gs17 0.184799857 0.070052354 0.3514429664 0.1732326612 -0.22022967 0.003214861 -0.405239687 -0.047291743 -0.24679440 0.160056459 0.08518827 -0.0463285866 -0.06034854 -0.30001767 -0.19348991 -0.035213712 -0.09465668 0.0759894988 0.1785756235 -0.132155045 -0.17500659 0.376832927 0.013218793 0.018574170 -0.110793912 0.229997712 0.16584921 0.05705518 -0.156772307 0.08025791
gs18 -0.187087483 0.337139118 0.1688542303 0.1173035568 0.05984658 -0.185941480 -0.119363637 -0.382728482 -0.15395065 -0.319451357 -0.19733920 -0.0144161899 0.24873343 -0.10552473 0.04524322 -0.001873581 0.22373606 0.0229936448 -0.3542996024 0.061859205 0.02839072 0.078164766 0.344304336 0.045874812 0.009125945 0.025623338 0.17909395 0.09353534 -0.131011234 0.06316538
gs19 -0.059003209 -0.199168662 -0.1837419847 -0.2237610050 0.39738058 -0.326919064 0.087628623 0.181877873 0.35191549 -0.027680315 0.24795143 -0.1101431952 -0.01839169 -0.16235495 0.08701808 -0.090546490 0.16014091 0.1263778250 -0.0780805378 0.230737817 -0.22144812 -0.217901043 -0.019311240 -0.228211869 0.086283799 -0.067073673 0.17863523 -0.10809469 0.095046484 0.11083758
gs20 -0.087459182 -0.195412041 -0.0130357705 0.2848639974 0.22802341 -0.158851672 -0.203819293 -0.074651734 0.26441584 -0.163246538 -0.16645128 -0.0007860099 0.23034725 -0.10381161 -0.44439333 0.400370645 0.17176277 0.0072304296 -0.0820074325 0.083326015 -0.18145094 -0.041971647 0.076837721 0.000302442 0.174386727 -0.151895543 -0.01190509 0.10267278 -0.134531574 0.19114066
gs21 0.107602195 -0.142208461 -0.1560412602 0.1057618700 0.08242831 -0.094411152 -0.402862002 -0.372859070 0.03195170 -0.056225322 0.02369290 -0.0133280573 -0.19355100 -0.27795918 -0.03191200 0.364990768 0.28739587 0.1564537944 0.0719681085 0.169215470 0.29072561 -0.251367594 0.063227672 0.159273607 -0.096533492 0.163138228 0.01013211 -0.06972215 0.049191913 0.02183063
gs22 0.281156732 -0.185969190 0.1466983344 0.0988277638 -0.05639434 0.008345487 0.314359229 -0.035846835 -0.02674254 0.048462980 0.04194433 -0.2929134701 -0.02180503 0.16130641 -0.09628426 0.094556572 -0.17393215 -0.0501843811 0.0418822082 -0.042590804 0.17563655 -0.241418448 0.454068984 -0.195659705 -0.078786970 -0.020000914 -0.31312338 0.24019694 0.013901423 -0.28969152
gs23 0.287000160 -0.009577127 -0.0258026809 0.3978394227 0.06574872 0.165351593 0.202895394 -0.008028034 -0.07998444 0.210698794 0.07377611 -0.0586860376 -0.15454336 0.13418397 0.08296051 -0.055745695 -0.06072953 0.0004303990 -0.0731050722 -0.109362156 0.03413574 -0.043312239 -0.067080708 -0.310656179 -0.124265593 -0.262454623 -0.54504850 0.22851199 0.123089583 -0.01824042
gs24 0.226216800 -0.073685267 -0.0417664264 -0.0006964549 0.18170065 0.466969874 0.008804967 -0.038827882 0.15703216 -0.158480858 -0.21933991 -0.0418454781 0.08244118 0.05264244 0.19388981 0.261405034 -0.08604337 -0.2537728142 0.0002742249 0.022868190 -0.15317303 -0.197659709 0.102648478 0.127786731 -0.008318546 -0.272121666 0.17408086 0.09227398 -0.213205479 -0.39209848
gs25 -0.227611755 0.023775737 0.0723240408 -0.1495365735 0.06081540 -0.172945821 -0.104641914 -0.283228744 0.09443370 0.264032568 -0.30609675 0.1905985693 -0.15253022 0.33940139 0.05489225 0.083252511 0.19734533 -0.0236399481 0.2777489932 0.036835483 0.17108518 -0.190520756 0.150268031 -0.160683713 0.167731621 -0.006525896 0.10202510 0.02616628 -0.376857271 -0.15791283
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+ grep("^REACTOME", names(c2BroadSets)),
+ grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- plageParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+ minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.11442430 0.32079541 0.19023827 -0.16386259 -0.34124516 -0.08626990 0.006244354 -0.09133096 -0.07958067 -0.19080877 -0.129759539 -0.011392352 -0.053528324 0.137113192 0.122790549 0.185113826 0.255475291 0.289729331 -0.231805083 -0.10599439 -0.16563165 0.254730153 0.28736502 -0.07380857 -0.13262739 -0.00202695 -0.12848634 0.04738066 0.15451669 -0.042949836 -0.1917455098 -0.158789670 -0.030545427 0.1681240794 -0.02372029 -0.0981317670
KEGG_CITRATE_CYCLE_TCA_CYCLE -0.14376128 -0.40210177 -0.10732752 0.22556600 0.22044109 -0.04149364 0.082632466 -0.03088703 -0.10141600 0.21634351 -0.099937129 -0.238283100 0.059799913 -0.044056815 0.106146035 0.035855219 0.056963046 -0.091694988 -0.111915190 0.08270476 0.17136294 0.002778763 -0.17116078 0.04310892 0.38606731 0.26041385 0.18985748 -0.28660545 -0.22184771 -0.072806417 0.0353622058 0.097891536 -0.169106885 0.1413099205 -0.11591220 0.0357089449
KEGG_PENTOSE_PHOSPHATE_PATHWAY -0.16235500 -0.32582108 -0.11076423 0.23827639 0.33496725 0.02867445 0.017174780 0.06591909 0.10482653 0.18448109 0.051993550 -0.025185654 0.117266799 -0.086462365 -0.121860074 -0.309601472 -0.202595001 -0.203907440 0.166706699 0.13841854 0.05621760 -0.217255930 -0.23400863 0.03480311 0.03693621 0.18017005 0.17067361 -0.14698325 -0.15401687 -0.039631290 0.1852566211 0.251925461 0.059502652 -0.1710616230 -0.05714658 0.1444660100
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS -0.19045563 -0.30144436 -0.06208281 0.23907573 0.23514442 -0.11949500 0.256530147 -0.15784897 -0.07002696 0.18754970 -0.156566301 -0.233437891 -0.028875826 -0.135832499 0.007013319 -0.063573306 -0.045190431 -0.134951243 -0.119095747 0.08957830 0.20494217 0.014625096 -0.21685204 0.12579094 0.30068903 0.30284667 0.20017848 -0.22704585 -0.03911287 0.152821859 -0.0118501734 0.195309455 -0.129960080 0.0414442346 -0.05624288 -0.0535986719
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.08708061 0.36924639 0.16317478 -0.18733952 -0.22969884 -0.07403687 0.005513622 -0.13403336 -0.10757766 -0.11347043 -0.126968905 -0.068529526 -0.073097377 0.145409314 0.117559506 0.192280283 0.262745324 0.261030448 -0.187064190 -0.10806619 -0.21446933 0.264815017 0.32316348 -0.02316450 -0.08242710 0.09121413 -0.08115837 -0.06082489 0.05128248 -0.096144492 -0.1729482337 -0.179767986 0.079378632 0.2025544282 -0.14107384 -0.1545868541
KEGG_GALACTOSE_METABOLISM 0.13896759 0.33236986 0.15287628 -0.19570500 -0.37392490 0.03112239 -0.101122302 -0.02357435 0.03161318 -0.18551649 0.042859194 0.003683625 0.058836073 0.058593014 0.103013057 0.136717007 0.125649307 0.257519495 -0.059380958 -0.09369887 -0.16262023 0.145102780 0.38948984 -0.18103028 -0.24299641 -0.04474028 -0.20609816 0.05089387 0.23425714 -0.067198742 -0.1327201321 -0.208840024 -0.007338931 0.1015346567 0.02976531 -0.1383576213
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.08699846 0.02769904 0.03088309 -0.15783874 -0.16132270 0.07393045 -0.152562581 0.17928005 0.15457917 -0.11563182 0.248868576 0.203636007 0.038899707 0.177895808 -0.087598070 0.024330837 -0.068874923 0.166621148 0.195566178 -0.09919733 -0.51840256 -0.125338656 0.15816739 -0.06627634 -0.24722350 -0.12644374 -0.27029081 0.23656458 0.03682528 -0.172195675 0.1255991760 0.010036282 0.146200884 -0.1183297380 0.06921028 0.0957347869
KEGG_FATTY_ACID_METABOLISM 0.25246920 0.21487789 0.06756412 -0.24015561 -0.15971798 0.04164973 -0.134634522 0.18133621 0.18742246 -0.09879733 0.059789040 0.211657105 -0.189741758 0.051073442 -0.063493728 -0.055876110 -0.064518498 0.032865183 0.144745872 -0.12747677 -0.34740988 0.017286592 0.07659859 -0.12250954 -0.14145045 -0.32332540 -0.30311340 0.30156896 0.14235300 -0.020396100 0.1491018982 -0.054180990 0.209632783 -0.0622606872 0.15856855 0.0084981268
KEGG_STEROID_BIOSYNTHESIS -0.26848204 -0.15151075 0.27196342 0.20005723 0.05633948 0.06709033 -0.076856972 -0.08144521 -0.11182014 0.23060319 0.031572540 -0.043182612 0.162334518 -0.113794316 -0.221396081 0.039299968 0.198596097 -0.125931968 -0.101950870 0.12788728 0.03906626 0.135077658 -0.01696710 0.13279903 -0.12493729 0.40294067 0.30898303 -0.07471426 -0.07229951 -0.346954681 -0.0425758777 -0.008173547 -0.157861540 -0.0398692105 -0.24333940 0.0194526802
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 0.22788265 0.27727244 0.12605512 -0.15231262 -0.07420505 0.10099690 -0.110400990 0.02784962 0.28647176 -0.07980438 0.173249992 0.174422862 -0.001563672 -0.107332599 -0.175605638 -0.211736911 -0.291012627 0.054097637 0.082675881 -0.19222910 -0.13208641 0.074845949 0.13658238 -0.04373454 -0.29216427 -0.25438809 -0.14526442 0.35661858 0.13638691 0.113474381 -0.0882569668 -0.027551600 0.137701542 -0.1643334547 0.08505740 -0.0276586587
KEGG_STEROID_HORMONE_BIOSYNTHESIS 0.22975311 -0.04610095 0.10063919 0.12299358 0.03877036 0.13465162 0.088715672 0.03494038 0.14951930 -0.05843410 -0.117297356 0.306369502 0.111144794 -0.204491028 -0.060894682 -0.033714074 -0.112850883 0.124922513 -0.016199947 -0.31755512 -0.07037955 -0.124619972 0.26355333 -0.17914396 -0.22832643 -0.07349334 -0.47727891 0.09134310 0.19265056 0.233158643 -0.0247334479 0.032853743 0.146944492 -0.1899024173 -0.01884571 -0.0486620136
KEGG_OXIDATIVE_PHOSPHORYLATION 0.04757384 0.42969714 0.09223380 -0.31361918 -0.22482181 0.17872708 -0.156175716 0.03456549 0.07932693 -0.18222063 0.263950703 0.156720262 -0.054368092 0.125986316 0.006787002 -0.084583991 -0.046388261 0.156195922 0.171548956 -0.20861678 -0.19200932 -0.036138327 0.17882865 -0.06323935 -0.25938295 -0.15467774 -0.19415965 0.14534418 0.07217123 -0.002104513 -0.0639220237 -0.134737904 0.153885773 -0.0408505217 0.22491981 -0.1064463186
KEGG_PURINE_METABOLISM 0.20065318 0.29721544 0.19035916 -0.18768395 -0.14876802 0.07499662 -0.111130384 0.04279520 0.10058079 -0.18253753 0.104394237 0.237489023 -0.156272735 0.004695238 -0.018444109 0.010848786 -0.031681573 0.100509407 0.200116332 -0.20128343 -0.13295068 0.008116163 0.13517872 -0.16149991 -0.22650307 -0.34997849 -0.25612139 0.34931922 0.23373805 0.081067825 0.0055786780 -0.137452124 0.043582088 -0.1302252071 0.06943792 -0.0581394776
KEGG_PYRIMIDINE_METABOLISM 0.21386387 0.31876668 0.13823771 -0.14977881 -0.22350466 0.05640788 -0.109066678 0.08462733 0.05200829 -0.09300310 0.030350113 0.314550177 -0.257314444 0.018989332 0.005829506 0.037731104 0.070314765 0.162687671 0.059216742 -0.19130213 -0.19705259 0.038453179 0.10999248 -0.11951467 -0.20321833 -0.33534029 -0.21755611 0.34102133 0.23875776 0.060935006 -0.0074629043 -0.180715242 0.033546687 -0.0939514779 0.01458195 -0.0220880991
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM -0.20681031 -0.37748716 -0.12565805 0.26798513 0.26914186 -0.12685519 0.153416637 -0.01650182 -0.14404837 0.28618661 -0.253033160 -0.185735835 0.033980001 -0.059404347 -0.042798179 0.052827743 0.087918043 -0.047097005 0.002603537 0.12045456 0.02098204 -0.038730195 -0.18413718 0.08243411 0.13850374 0.35054894 0.23717572 -0.12482694 -0.12337093 -0.048174199 0.0483989160 0.232747019 -0.087796534 0.0098209646 -0.20356325 0.0009030612
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.01555983 0.39948710 0.26524975 -0.11344673 -0.30536311 0.13871948 -0.119877999 0.01826166 0.03199101 -0.13884023 0.000402732 0.228057870 -0.065492316 0.046027102 -0.120910813 -0.112044381 0.107682776 0.280525919 0.062717644 -0.08761679 -0.31120689 0.045531608 0.16292802 -0.12689384 -0.31176258 -0.11566649 -0.04943121 0.14634414 0.17297063 -0.064286408 -0.1019910400 -0.192809929 0.239116210 0.0222125604 -0.07591641 0.0297711570
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.14011533 0.44950137 0.13715860 -0.21286365 -0.25951992 0.03554671 -0.035671613 -0.01235037 0.10835898 -0.19692749 0.119707919 0.229911107 -0.124986706 0.071248763 -0.050382477 0.112207174 -0.038781286 0.141432934 0.158050492 -0.24246930 -0.20193494 0.019331667 0.10357964 -0.11758175 -0.13149796 -0.30066366 -0.23406437 0.28585381 0.13769399 0.074084706 0.0009278377 -0.149035605 0.067135796 -0.0470514419 0.08543382 -0.1214980980
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.18341492 0.34228948 0.05029107 -0.34818659 -0.10685182 0.09265336 -0.088466493 0.11016160 0.15517234 -0.26698602 0.224420582 0.146464701 -0.044408678 0.093719606 0.048431770 -0.038893096 -0.147876699 -0.001782784 0.121902396 -0.03997209 -0.15444379 -0.033776069 -0.00457758 -0.03957663 -0.17241854 -0.33220603 -0.31794663 0.27603631 0.13609807 0.092390238 0.0150196645 -0.116601679 0.108012207 -0.1542070774 0.21229246 0.0004075145
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS -0.14556385 -0.10361716 0.22024326 0.31503617 0.06126010 -0.11154855 0.086414704 0.09990315 -0.15911865 0.25419971 -0.371443880 0.088126533 -0.008249792 -0.058022569 -0.290894975 -0.038124927 0.289981591 0.243192257 -0.230345230 -0.15276445 -0.12892010 0.072417276 -0.01986629 0.04301764 -0.08484861 0.12551261 0.03154033 -0.09408278 -0.02997378 -0.054032625 0.0911418987 0.151438348 0.140147297 0.0839960430 -0.34942241 0.0332716988
KEGG_LYSINE_DEGRADATION -0.27646705 -0.27151298 -0.14559260 0.23343969 0.37761951 -0.14982544 0.071650219 -0.03606215 -0.11370614 0.13919560 -0.059279394 -0.148559519 -0.055897641 -0.004205009 -0.084549331 -0.125562528 -0.038538048 -0.095318136 -0.053812331 0.06965729 0.21281299 0.081810273 -0.18178297 0.22842373 0.26345436 0.22182994 0.31463356 -0.21013663 -0.18109835 -0.054938949 0.0360631509 0.177937829 -0.061732716 0.0873730291 -0.14374132 -0.0235819496
KEGG_ARGININE_AND_PROLINE_METABOLISM -0.16123111 -0.13057226 -0.11107844 0.02273494 0.21356398 -0.07436990 0.084384101 -0.16407155 -0.25289315 0.14391482 0.036172848 -0.326582857 0.055461961 0.147752762 0.096612753 -0.119843646 -0.098278801 -0.122948974 -0.211625005 0.19972609 0.33443209 0.139927393 -0.24553021 0.20165627 0.28074920 0.22470401 0.20124083 -0.21576039 -0.19741636 -0.022915154 -0.0511405637 0.032249241 -0.025522833 0.1225511902 -0.02111686 0.0150635951
KEGG_HISTIDINE_METABOLISM -0.38691525 -0.08953562 -0.10044464 -0.01426187 0.01496539 -0.13622135 0.073354885 -0.08532239 -0.06721292 -0.02768174 0.076490066 -0.047484587 0.166533226 0.046557442 0.088751653 0.005292349 -0.081057843 0.067987559 -0.094320047 0.21609906 0.44120825 -0.100792083 0.13452155 0.08461381 -0.02486270 0.31367516 0.26079310 -0.32426284 0.10030542 -0.211640562 -0.0433522226 0.176759090 -0.192709853 0.0459120461 -0.22119461 -0.0645469418
KEGG_TYROSINE_METABOLISM -0.32712829 -0.42822607 -0.12167600 0.02926148 0.09223972 -0.04442842 0.021231012 0.02765216 -0.03822786 0.04965165 0.123045871 -0.128743087 0.217063631 -0.020137764 -0.074664972 -0.110309150 0.009697748 -0.014759694 -0.068874216 0.21673625 0.25233361 -0.119479733 -0.10033969 0.17709985 0.13429743 0.33966951 0.19420105 -0.33874057 -0.09490785 -0.124655343 0.1026505643 0.260903234 -0.098142875 0.0001200643 -0.07224524 0.0778319820
KEGG_PHENYLALANINE_METABOLISM 0.40967474 0.19836523 0.08736858 0.02869842 -0.01374240 -0.09317232 0.234731915 -0.10208931 -0.02436911 -0.04192146 0.046894702 -0.010923766 0.047580560 0.042336433 0.092609398 -0.004019050 -0.309686433 -0.136083760 0.434626863 -0.10463787 -0.38590280 -0.094165597 0.21855328 -0.17952300 -0.11488955 -0.05718921 -0.22158783 -0.01384747 0.01198482 -0.007884161 -0.0977790774 0.182631715 0.047187141 0.0992475649 -0.03286374 -0.1362134528
KEGG_TRYPTOPHAN_METABOLISM 0.15935872 0.31858549 0.09156412 -0.23847420 -0.09302019 0.08275092 -0.025728297 0.07322292 0.19026430 -0.13868036 0.206619445 0.128988091 -0.078007790 0.096592856 0.011962634 -0.051351485 -0.180762468 0.061269834 0.238903090 -0.09208227 -0.10207168 -0.106243834 0.06774698 -0.08751554 -0.26540552 -0.25036631 -0.51241085 0.26365030 0.06499509 0.024424527 0.0203047444 -0.027556007 0.180543189 -0.0780303726 0.07999529 -0.0340353504
> pickrellPar <- plageParam(pickrellCountsArgonneCQNcommon_eset,
+ canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esrnaseq[seq.int(min(nRowsToPrint, nrow(esrnaseq))),])
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS -0.15214812 0.19079795 0.0106548721 -0.06539635 -0.11195287 -0.04362555 -0.31151529 -0.07757363 0.4492669 -0.18037776 0.04612305 -0.0300515212 0.0095461535 -0.17685565 0.0346814651 0.2305611 -0.0811595896 2.228039e-02 -0.0263523574 -0.003290343 -0.17154720 0.13948803 0.0247698576 0.13773137 0.13227548 0.14302214 -0.11441695 0.3020346 0.07079582 -0.052860583 -0.4212291 0.15020276 0.16979426 -0.1934081 0.003119229 -0.0533843888
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.15203505 -0.17111274 0.0192425535 0.05927134 0.10807196 0.11312140 0.28808722 0.12139802 -0.4880436 0.15299104 -0.04906447 -0.0147576258 0.0316875534 0.11937406 0.0089518864 -0.2637738 0.0406273352 -4.893202e-02 0.0399987391 0.020132090 0.24689245 -0.14284022 0.0008861416 -0.16483674 -0.08846222 -0.14421236 0.18663124 -0.3056940 -0.10053188 0.025582990 0.2761436 -0.11072658 -0.17974086 0.2615204 0.021548560 -0.0214665332
KEGG_PENTOSE_PHOSPHATE_PATHWAY -0.15765014 0.18674949 -0.0273930657 -0.07307133 -0.10533768 -0.09164663 -0.32248478 -0.11596237 0.4765833 -0.14616308 0.04285343 -0.0546959513 -0.0078616045 -0.15559699 0.0056289676 0.2402897 -0.0654167765 9.649199e-03 -0.0248954667 0.014836184 -0.19279004 0.15939724 0.0142917986 0.15493177 0.12077530 0.12820289 -0.13375282 0.3157634 0.06478541 -0.032853560 -0.3012578 0.15637181 0.18509625 -0.2567167 0.011332850 -0.0219922268
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS -0.09948024 0.17081884 0.0007132175 0.03385509 -0.06241216 -0.10503442 -0.20057306 -0.07219669 0.3963326 -0.12678766 0.06517810 0.0224058492 0.0671487290 -0.18608845 0.0013261299 0.2291769 -0.0210756261 2.665083e-02 -0.0991881059 -0.005604071 -0.49238630 0.15844499 0.0684573628 0.18159133 0.06988761 0.19261084 -0.14240752 0.2382392 0.02679420 -0.052668574 -0.3419867 0.13615421 0.10134608 -0.2093921 -0.007625566 0.0377750733
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.11684514 -0.15932375 0.0424584303 0.08863850 0.01606414 0.07687084 0.26942124 0.09040454 -0.4770715 0.19043992 -0.02814712 0.0084783419 0.0113907130 0.11293532 0.0081665138 -0.2110960 0.0520711362 5.324071e-05 0.0002572043 0.004341436 0.20787937 -0.14010382 -0.0237929613 -0.14074488 -0.11101353 -0.11615857 0.13347359 -0.3440427 -0.08201004 0.014824329 0.4008495 -0.13645213 -0.18798271 0.2656192 0.001164264 0.0452927563
KEGG_GALACTOSE_METABOLISM -0.10572541 0.20093414 -0.0337689448 -0.06828622 -0.05141289 -0.04603842 -0.27803249 -0.08715881 0.4593304 -0.16948100 0.02158359 -0.0228842754 -0.0251350377 -0.13562816 -0.0336397673 0.2240697 -0.0559377116 3.578987e-02 -0.0187799930 -0.009111103 -0.19168860 0.14544677 0.0582003469 0.14876379 0.04249027 0.08803668 -0.15131539 0.3368992 0.07977192 -0.004153293 -0.4096545 0.16989169 0.19432462 -0.2523470 0.001213619 -0.0565674873
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM -0.18741437 0.16387617 -0.0060310939 -0.03859070 -0.14802565 -0.06396724 -0.33253815 -0.09961008 0.4362764 -0.27301158 0.09626864 0.0270197462 0.0232057101 -0.31223804 0.0187798020 0.2361106 -0.0726098042 -4.028766e-03 -0.0969205827 0.054098119 -0.09624125 0.17262148 0.0381393930 0.13351280 0.05969382 0.20522582 -0.04629863 0.2630025 0.13133577 -0.077179005 -0.3109268 0.07680757 0.15756403 -0.1319563 0.004626489 -0.0005768344
KEGG_FATTY_ACID_METABOLISM 0.14404628 -0.17549826 -0.0168733006 0.03662427 0.13805007 0.13510632 0.29212490 0.11769787 -0.4538781 0.16997502 -0.05292794 -0.0171357447 0.0056091986 0.20068593 -0.0171192068 -0.2391582 0.0523800221 -3.355725e-02 -0.0037541309 0.007606301 0.26720390 -0.13680786 -0.0229006319 -0.12955701 -0.16649337 -0.18843753 0.11227260 -0.3030089 -0.07180728 0.065746889 0.3537898 -0.09725041 -0.16000999 0.1584219 0.002131614 0.0267022633
KEGG_STEROID_BIOSYNTHESIS -0.23993046 0.13867049 0.1187377626 0.05110320 -0.13720084 -0.17477296 -0.20358441 -0.12237759 0.4362713 -0.01023068 0.09255610 0.0831711016 -0.0316845885 -0.09055792 -0.0101667462 0.2066797 0.0664619590 6.476799e-02 0.0581287322 0.001741120 -0.22245981 0.14966908 -0.0538040397 0.16575480 -0.03806247 0.08839711 -0.09754098 0.3146994 0.09568740 -0.024727977 -0.3582404 0.08721987 0.08303645 -0.3500921 -0.182876427 0.0455568716
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS -0.10378950 0.13345241 0.0602863571 -0.16623904 -0.07063215 0.01365008 -0.19534754 -0.17435286 0.4708230 -0.07118342 0.11618557 -0.0502633451 -0.0554177755 -0.16614665 0.0076810221 0.2090015 0.0672454536 3.512318e-02 -0.0428960078 -0.024698829 -0.33368337 0.14917398 0.0139906079 0.08658955 0.10773984 0.14806389 -0.11894824 0.3430318 -0.01837218 -0.088410625 -0.4130314 0.11951559 0.13746845 -0.1309977 -0.048676576 0.0540649156
KEGG_STEROID_HORMONE_BIOSYNTHESIS -0.21197941 0.18630856 0.0301018384 -0.11630509 -0.04474517 -0.08691530 -0.11027761 -0.11733030 0.4409750 -0.20162476 0.13665328 0.0221236331 -0.0003285179 -0.14428211 0.0620844698 0.1180512 0.0562025241 1.740092e-01 -0.0893062456 0.018200638 -0.29453200 0.08782095 0.0795061796 0.14770804 -0.04685136 0.10482351 -0.13782587 0.3286641 -0.01216641 0.001473664 -0.4633424 0.07796440 0.16692838 -0.1512924 -0.030595788 0.0201011702
KEGG_OXIDATIVE_PHOSPHORYLATION 0.11392670 -0.15176080 -0.0078716193 0.03185503 0.08755261 0.16899727 0.27816007 0.10828366 -0.4984539 0.15443204 -0.05388480 -0.0005382922 0.0143975861 0.13323583 -0.0144179595 -0.1631206 -0.0012127107 -4.539461e-02 0.0435086752 0.022640863 0.29947218 -0.13776551 -0.0302126129 -0.18067891 -0.13765087 -0.16335643 0.12104839 -0.3312689 0.02163840 0.030604155 0.3449082 -0.11292053 -0.11048607 0.2310232 -0.025202957 -0.0394868208
KEGG_PURINE_METABOLISM 0.14576228 -0.17970119 0.0695643645 0.07390013 0.09426888 0.14811626 0.25313045 0.12971197 -0.4997313 0.16664358 -0.06909949 -0.0011720262 -0.0279803304 0.13994248 0.0019350762 -0.1746847 0.0245422008 -6.364770e-02 0.0941657279 0.013648424 0.26762396 -0.16851615 -0.0456918476 -0.19287243 -0.08967612 -0.14275219 0.16046531 -0.3211839 -0.02696631 0.051340413 0.2707759 -0.12761083 -0.17070100 0.2401788 -0.012335268 -0.0313934410
KEGG_PYRIMIDINE_METABOLISM -0.15527782 0.18681216 -0.0710134938 -0.09272258 -0.09107116 -0.15945406 -0.26422713 -0.13051958 0.4924685 -0.17590868 0.06869025 0.0017294883 0.0440173962 -0.15137425 -0.0069782437 0.1818896 -0.0252424604 5.910549e-02 -0.0641390004 -0.009211103 -0.25500824 0.17506163 0.0368705159 0.19122864 0.11892819 0.15054298 -0.17164591 0.3047345 0.02982096 -0.059310144 -0.2438609 0.10353402 0.16710577 -0.2540935 0.041640375 0.0268777463
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.16187518 -0.15242447 0.0445845851 0.03801959 0.16815027 0.15816036 0.18629258 0.13647099 -0.4547896 0.15764760 -0.09834758 -0.0673653703 -0.0327515803 0.13813612 -0.0001154741 -0.2242866 -0.0035237558 -8.144324e-02 0.0846143930 0.016951778 0.35755319 -0.12650621 -0.0869564600 -0.15472376 -0.13565892 -0.15047719 0.19304761 -0.2923463 -0.10340182 0.124156397 0.2929275 -0.08529239 -0.17347808 0.1458381 0.019564617 -0.0001020227
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.18425567 -0.21997777 0.0792549975 0.02796617 0.15066508 0.13108206 0.09096202 0.09603363 -0.4087696 0.19271142 -0.11346497 -0.0412294265 -0.0825276719 0.25407808 -0.0336109990 -0.1920607 -0.0511250493 -1.385250e-01 0.0965515196 -0.005825203 0.28983157 -0.12541010 -0.0631413865 -0.18063408 0.07210946 -0.15207612 0.12502562 -0.3434555 -0.08266163 0.241050135 0.2367705 -0.13650734 -0.16052837 0.1219852 0.122337569 0.0188602175
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.21582742 -0.19257267 0.0481026570 0.12532384 0.12863263 0.12702487 0.21916790 0.14145654 -0.4628510 0.18903573 -0.08990904 -0.0356654022 -0.0293211714 0.21616290 0.0113339421 -0.2359683 0.0240081539 -8.452455e-02 0.0615230196 -0.031731840 0.26949610 -0.14960573 -0.0490440852 -0.18626782 -0.06807870 -0.13588057 0.13260775 -0.3153507 -0.07004173 0.095123437 0.2314867 -0.12190522 -0.17317799 0.1942247 0.001740289 -0.0003819966
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION -0.13320980 0.19146649 0.0001692046 -0.04724794 -0.11203115 -0.10900765 -0.32384751 -0.08670029 0.4661106 -0.15194445 0.02163166 0.0263972205 -0.0156839833 -0.23372426 0.0016790308 0.2330446 -0.0339518900 2.867854e-02 -0.0347112069 -0.013832614 -0.26086893 0.15508615 0.0463970898 0.12786410 0.13562535 0.16840661 -0.11800503 0.3056234 0.08931534 -0.062290601 -0.3304639 0.11023004 0.15287141 -0.1761863 -0.010338119 -0.0065512747
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS -0.18497233 0.17649821 0.0506236410 -0.08746720 -0.15678895 -0.18326441 -0.19998683 -0.08831954 0.4498416 -0.09855080 0.04904952 0.0387063020 0.0391040897 -0.19473731 -0.0088725559 0.2294151 -0.0153974275 8.110413e-02 -0.0361551097 -0.038686397 -0.29902619 0.15638790 0.0813030069 0.15365219 0.07778971 0.14702327 -0.22562370 0.2961998 0.06095390 -0.060339944 -0.3294075 0.14871582 0.15615268 -0.1661644 -0.018031872 -0.0007282847
KEGG_LYSINE_DEGRADATION -0.14840078 0.19887266 -0.0896794806 -0.05874662 -0.09522200 -0.16067588 -0.25024857 -0.12714531 0.5089357 -0.17188541 0.06501566 0.0211715670 -0.0087000106 -0.11468731 -0.0192207645 0.1887464 -0.0086852919 9.220565e-02 -0.0997662839 -0.015545295 -0.25889646 0.14938001 0.0102360429 0.15953226 0.08245914 0.11756512 -0.12447080 0.3428059 0.05803155 -0.041416622 -0.2706288 0.11974209 0.19925355 -0.2252852 -0.018670642 -0.0059757956
KEGG_ARGININE_AND_PROLINE_METABOLISM -0.15599441 0.17162854 -0.0165755907 -0.04984281 -0.13252570 -0.13503025 -0.24149898 -0.12496608 0.4652361 -0.18264708 0.06245441 0.0533993450 0.0200002688 -0.17588537 0.0187300201 0.2268855 -0.0308582433 6.457058e-02 -0.0409831672 -0.022302704 -0.26703092 0.13286020 0.0597241639 0.15221801 0.12299299 0.13822870 -0.16751098 0.3220956 0.08792924 -0.097087427 -0.3352892 0.08674901 0.18213748 -0.1854224 -0.015128027 0.0087392720
KEGG_HISTIDINE_METABOLISM -0.16341627 0.21211137 -0.0597047650 -0.07019812 -0.06569836 -0.16907760 -0.24238369 -0.09397806 0.4720904 -0.22248144 0.09449529 0.0337872241 0.0814929382 -0.14765066 0.0166344423 0.1896539 -0.0151032687 7.080535e-02 -0.0387446192 -0.034208862 -0.28356932 0.13501819 0.0592272252 0.14530433 0.09060491 0.16483382 -0.08830364 0.3105553 0.03130984 -0.076375024 -0.3379780 0.10320490 0.12281655 -0.2312373 -0.020753794 0.0269168631
KEGG_TYROSINE_METABOLISM -0.10093863 0.18267763 -0.0242538303 -0.06443060 -0.02632197 -0.16928691 -0.21835995 -0.12802624 0.4897721 -0.20718144 0.08915284 0.0230208339 0.0685731978 -0.11497401 0.0264683523 0.1715784 -0.0240623350 5.461238e-02 -0.0359349395 -0.041186627 -0.34571344 0.11565207 0.0429404806 0.15350966 0.12352853 0.16156040 -0.14241499 0.3437890 -0.02098569 -0.034677062 -0.3320536 0.12420589 0.08212171 -0.1959923 -0.039814920 0.0134459864
KEGG_PHENYLALANINE_METABOLISM -0.13596282 0.06742145 0.0882449903 -0.02244406 -0.09867622 -0.06439912 -0.08447981 -0.15306648 0.4203738 -0.10031185 0.17368849 0.0780588540 0.0996577430 -0.02544390 0.0171562407 0.1211227 0.0235791297 8.347408e-02 -0.2466780511 -0.006247915 -0.61710863 0.07252436 0.0317753835 0.10302349 0.06683344 0.11139551 -0.15093291 0.2664307 0.04334024 -0.011422551 -0.1744265 0.11107338 0.02648540 -0.2152238 0.019167613 0.0819975622
KEGG_TRYPTOPHAN_METABOLISM 0.17049240 -0.19170650 0.0004630847 0.05089247 0.12593277 0.11515466 0.27670376 0.12909756 -0.4814202 0.17977370 -0.06320424 -0.0194461931 0.0070929693 0.19100894 -0.0230060896 -0.2042648 -0.0001048516 -7.878183e-02 0.0931404987 -0.026808640 0.24465868 -0.13838085 -0.0248749524 -0.16243909 -0.09741608 -0.15878157 0.07600539 -0.2897865 -0.09352519 0.056621625 0.3530154 -0.08401918 -0.15938269 0.2105366 0.043211634 -0.0264526019
>
> gbmPar <- plageParam(gbm_eset, brainTxDbSets)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up 0.009503434 -0.07148275 0.03702570 -0.1449671 -0.06040476 -0.07594821 -0.08471232 -0.011938741 0.02993423 0.065023141 0.01762836 -0.11912551 -0.05949992 0.00525537 -0.05523948 -0.05372246 -0.08443369 -0.08598174 -0.11875051 -0.042058976 -0.04030687 -0.085476621 -0.10685594 0.02611153 0.04356317 -0.0705649980 -0.006844708 -0.01728745 -0.05473265 -0.02670516 -0.023271397 0.028072017 -0.03921781 -0.10235048 -0.05010187 -0.07005158 -0.09209016 -0.10881587 -0.05062336 -0.007877207 -0.08243841 -0.06962198 -0.08767648 -0.02583498 -0.04666987 -0.07810986 -0.01152421 0.02981450 -0.08655273 -0.024763415
astroglia_up 0.047878697 0.13259958 0.09353196 0.1723954 0.05397369 0.09437815 0.12333017 0.034441261 -0.02691552 0.082648790 0.05525398 0.07854437 0.02675066 0.14436470 0.03635936 0.07445693 0.18500914 0.12978579 0.10685532 -0.046038185 0.03640657 0.134998687 0.14571431 0.16997016 0.02481540 0.0363660300 -0.020974725 0.08501924 0.13807016 0.11677809 -0.008999474 -0.020349973 0.05204384 0.04461865 0.09432334 0.05564952 0.05441292 0.07187041 0.06496384 -0.016408375 0.06458610 0.08187014 0.14767961 -0.01197801 0.03687600 0.06445718 0.01797752 0.01595298 0.09244863 0.052499964
neuronal_up -0.109710924 -0.01702066 0.01301810 -0.0150155 -0.09724660 0.02146057 0.05010519 -0.040146081 -0.06066290 -0.006770987 -0.11536936 0.07187279 0.06404673 0.05934842 0.01706701 0.06703005 -0.05028874 0.06844218 0.03520158 -0.007305407 -0.02100709 -0.009551983 -0.02286479 0.02104686 0.02714991 0.0009992218 -0.091286596 0.04988690 0.05224805 0.04092799 -0.012195643 0.009698397 -0.03329177 -0.03730078 -0.06501777 0.00777109 -0.01276343 -0.07101898 -0.03167425 0.008950496 -0.04525475 0.03152291 -0.05007149 -0.06206634 0.00277177 0.05362907 0.06015409 -0.12476908 0.01965553 -0.006541254
oligodendrocytic_up -0.053316262 -0.03076570 -0.13026183 -0.1054244 -0.15884604 -0.04584733 0.01162552 -0.008735686 -0.07831724 0.029790216 -0.12264757 -0.17633055 -0.22829418 -0.09563053 0.01913198 -0.08062237 0.06710752 -0.04973426 -0.09459566 -0.035043759 -0.07087794 -0.024834220 -0.14132943 -0.08015759 -0.12351419 -0.1018570138 -0.145485987 -0.08031675 -0.13791221 -0.06314112 -0.055013638 -0.111969729 -0.06278656 -0.12395121 -0.11149668 -0.13560637 -0.03100847 -0.11540779 -0.19569986 -0.004032233 -0.09848717 -0.01310448 -0.01601479 -0.08806238 -0.15998008 -0.03256551 -0.02666356 -0.04873438 -0.04271502 -0.015764935
TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up -0.10887523 -0.07864038 -0.04197239 0.095668384 0.18776408 0.25307779 0.08792407 0.05994647 0.13261591 0.021215334 0.1151069 0.12610727 0.11787216 0.03692715 0.07098464 0.06193001 0.05640898 0.07437529 0.03446988 0.13673871 0.05740561 0.04951662 -0.03940410 0.07655210 0.08887779 0.06360155 0.063447530 0.09165828 0.10386274 0.098671883 0.08994742 0.14845583 0.05137301 0.101763991 0.0439691905 0.12523626 -0.05949182 -0.02266147 0.04146871 -0.01734481 0.02456185 -0.005848951 0.11898178 -0.003748745 0.04014935 0.049498323 0.0378446673 0.028926994 0.081286268 0.06431596
astroglia_up 0.13560615 0.06372746 0.09853784 -0.061051452 0.01577089 -0.04760733 -0.01301234 -0.02033879 0.03042881 0.007860558 0.1302317 0.04866147 0.11807311 0.02651416 -0.02576869 -0.02249800 0.03139450 0.01262743 0.10298674 0.04376961 -0.02441912 0.04007613 0.10426429 0.05984316 0.09531040 0.01361742 -0.006054302 0.01417130 0.01785855 -0.024485729 0.04885270 0.04978712 0.01089287 -0.003688539 -0.0255875216 -0.05318817 0.01572855 -0.04017804 -0.01581070 0.08027547 0.06475093 -0.019267885 -0.01000033 -0.012468882 0.03808888 0.016444129 0.0004891894 0.006058522 0.001277776 0.04623002
neuronal_up -0.01603674 0.03026768 -0.04846411 -0.081274578 0.03036729 -0.10588657 -0.04819897 -0.21472580 -0.07924660 -0.014852256 -0.3937604 -0.10090691 -0.42227945 -0.02226663 -0.03522747 -0.15937196 0.02880150 -0.03360695 -0.19537945 -0.02678998 -0.01237703 -0.05800257 -0.08946093 0.02804959 -0.33447989 -0.06646701 0.001490673 -0.06111592 -0.00788255 -0.005433944 0.08875419 -0.04552211 0.06832540 -0.054242676 -0.0165587308 0.03709143 0.08683758 0.07694510 0.00983925 0.05086959 0.03951686 0.046397028 0.03379387 0.065956603 0.07285765 0.002567756 0.0022974121 0.076873274 0.040563891 -0.04577361
oligodendrocytic_up -0.09082646 -0.03209598 -0.06775336 -0.001343057 0.09570037 -0.04469363 -0.03506036 -0.09033811 0.01079102 -0.008493560 -0.1060987 0.02222565 -0.09131953 -0.02902642 -0.01525947 -0.07435504 0.08049313 0.05654690 0.03601434 0.01580467 -0.08981765 -0.01162585 0.03884722 -0.00640505 -0.11088869 0.06651459 0.048149691 0.05667692 0.06740432 0.057691526 0.05627159 0.01676310 0.06553035 0.068221314 0.0005776113 -0.02757186 0.07961760 0.03639202 0.08426877 0.07545897 0.07456736 0.040406936 0.06787397 0.080378144 0.05427988 0.059627054 0.0040825991 0.039001591 0.038807887 0.01393330
TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up 0.10254985 0.1209366458 0.005457102 0.05470414 0.05324132 0.004583494 0.07287897 0.01803334 0.092298928 0.106581126 0.03911847 0.08760433 0.08083304 0.12273304 0.08658859 0.09439140 0.12859993 0.12899656 -0.05799326 0.043791271 -0.12734557 -0.07620178 -0.101627927 0.07398850 -0.14128439 0.04168816 -0.10586947 -0.07738761 -0.05189054 -0.04129260 -0.029881354 -0.02425999 -0.03083819 -0.01363261 -0.03413866 0.03369514 -0.02533095 -0.026089207 -0.05887989 -0.023565388 -0.02660048 -0.13175535 -0.131223466 -0.04934655 -0.07222247 0.04595771 -0.002484733 -0.02006267 -0.02129216 0.0121870804
astroglia_up 0.01473182 -0.0002823507 -0.041514372 -0.04221281 0.05781689 0.010362305 -0.03948686 -0.02292038 0.009218869 0.003819796 0.08805820 0.05787047 -0.04832227 -0.04771188 -0.03770525 -0.00397720 0.01702062 -0.04901255 -0.15053965 -0.066808334 -0.12029138 -0.13543562 -0.111383004 -0.11055588 -0.07080332 -0.05626645 -0.16040451 -0.06003255 -0.11320734 -0.07762499 -0.067457036 -0.06885981 -0.07206253 -0.09501078 -0.08210609 -0.14076913 -0.09259525 0.017705647 -0.07440865 -0.075879552 -0.10686648 -0.12383580 -0.109491916 -0.05092156 -0.12756381 -0.04676953 0.016467894 -0.08296504 -0.11449864 -0.0624475003
neuronal_up -0.05510838 0.0693924418 0.049907805 0.06579639 -0.03553495 0.060569667 0.04258533 0.05347991 0.011061722 -0.022561037 0.05657129 0.08324986 -0.06484210 0.05410708 0.08696189 0.04328396 0.04756120 0.05241028 0.03859840 0.004121992 0.05429824 0.06696186 0.039995573 -0.03731216 0.03871302 0.01346663 -0.02003846 0.03361013 0.08956373 0.05912840 0.004434217 -0.12181570 0.03493980 0.01353410 0.04421769 0.01083988 0.03740344 -0.008455138 0.03989240 0.043233261 0.03530835 0.04811405 0.067893057 0.06035066 0.05073357 0.04311893 0.074185702 0.05368352 0.04001603 -0.0368438811
oligodendrocytic_up 0.01488734 0.0588328752 0.073964840 0.05639762 0.06448371 0.103919757 0.05028910 0.07722783 0.094043741 0.035205083 0.07003096 0.06202171 0.04362975 0.05582357 0.08811635 0.07662414 0.06354034 -0.13317556 0.09801811 0.010237076 0.04782735 0.09917287 0.003572068 0.02818885 0.12062411 0.06959310 0.09380954 0.09824244 0.04046508 0.05673212 -0.016644605 -0.11809801 0.06714657 0.02817944 0.07503049 -0.01017455 -0.01208933 -0.031760653 -0.16273288 0.008979194 0.06577860 0.08468706 0.006857635 -0.03150528 -0.03036885 0.08254308 0.070749406 0.09400074 -0.01657986 -0.0003181655
TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up -0.12793182 0.05813961 -0.02996638 -0.03999179 -0.01317216 -0.06556770 -0.06014645 -0.10524550 0.03410507 0.03174620 -0.07131517 -0.03864651 -0.00656357 0.004862977 -0.05760770 -0.03220225 -0.14379979 0.006209294 0.01015281 -0.02506194 -0.15712941 -0.06978470 -0.039842096
astroglia_up -0.07509997 -0.03112873 -0.07460949 -0.10572792 -0.07367029 -0.08467325 -0.05192066 -0.04367356 -0.07272862 -0.06252615 -0.10738803 -0.07352765 -0.08211912 -0.086061829 -0.11834540 -0.05541622 -0.05335162 -0.071461495 -0.06913880 -0.14663735 -0.10229018 -0.04606975 -0.030543430
neuronal_up 0.04965757 0.03625217 0.04174849 0.04119978 0.04325152 0.04343971 0.04604542 0.03545067 0.04582293 0.07345420 0.01598958 -0.00251816 0.03897229 -0.071738618 0.06571136 -0.05706466 0.03314141 -0.016854947 0.07308937 0.04576623 0.03139639 0.06476292 0.047577132
oligodendrocytic_up 0.06265322 -0.03057294 0.08799201 0.04420027 0.07389345 0.10096870 0.02276466 0.04904987 0.08861485 0.09026904 0.06005119 0.02120084 -0.02586168 0.056221418 0.04705479 0.02053537 0.11599128 0.059425833 0.04519846 0.09306496 0.10243557 0.07848995 0.009634767
>
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> leukPar <- plageParam(leukemia_eset, cgpC2BroadSets,
+ minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP -0.1733940255 -0.033909950 -0.21494771 0.225895163 0.063750234 0.167895761 -0.120141623 -0.301364574 -0.127897961 -0.17662816 -2.033307e-03 -0.0580768131 0.22143221 -0.10332109 -0.22150927 0.043353690 -0.25639842 -0.09207537 -0.08853224 0.026931498 -0.14639547 0.099528895 -0.0728970131 0.20132393 0.071949059 0.065447939 0.14428259 0.131615034 -0.13550381 0.058275958 0.32869002 0.11720023 0.110313219 1.576915e-01 0.36374728 -0.052301552 -0.221995813
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP 0.0091056904 -0.007229294 -0.26682324 0.239296160 0.102079970 0.107282626 -0.220934366 -0.114993916 -0.242707246 -0.35282402 -1.319142e-01 -0.2908596517 0.19217905 -0.05096841 -0.30028124 0.081213713 -0.06235553 -0.03413274 0.14630064 0.233615255 -0.02563993 0.216233541 0.1512191200 0.18209821 0.096718310 0.012136911 0.05625600 0.144054943 0.15035428 -0.046779826 -0.05975187 -0.23316425 -0.056470909 -4.192709e-02 0.16251868 0.109530419 0.147564140
WINTER_HYPOXIA_UP 0.0834055313 -0.070653851 0.36411795 -0.247095973 -0.178229854 -0.221082475 -0.024371138 0.180921942 0.038462365 0.10271188 -6.399298e-02 -0.0082717873 -0.01821576 0.28000441 0.17834176 -0.050337001 0.11095592 0.07805238 0.10651755 -0.242836351 0.23470420 0.062017426 0.0444107834 -0.26140415 0.191019536 0.057727131 -0.25471951 0.003543483 0.20328048 0.027252717 -0.16090502 -0.15356573 -0.065566664 5.311727e-02 -0.35349585 -0.060628683 0.034808040
PYEON_HPV_POSITIVE_TUMORS_UP -0.1194662949 0.038017996 -0.28521866 0.275081686 -0.031488732 -0.038588970 -0.100533814 -0.297050611 -0.238634457 -0.29082863 -7.600985e-02 -0.2335338233 0.31515092 -0.08353618 -0.18336902 0.087151767 -0.20372452 -0.14291385 0.03273765 0.233092544 -0.04825298 0.113859039 0.0442618489 0.16991714 0.231386554 0.005267212 0.03397312 0.099018174 -0.04752945 0.167145951 0.12918791 -0.11535230 0.055991634 8.848689e-02 0.24812128 0.117475851 0.050707009
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP 0.1198739462 0.187824071 0.39422522 -0.345600421 -0.152731606 -0.106308076 0.142740956 0.120710037 0.111680385 0.07724317 -8.733673e-03 0.0899926339 -0.06187972 0.35041893 0.14911728 -0.027779682 0.08478613 0.05561965 0.01558144 -0.248802758 0.23046261 0.041120203 -0.0006047729 -0.26801992 -0.003634823 0.026561742 -0.21188895 -0.043144995 0.07637875 -0.133457745 0.15331729 -0.05186474 -0.076486263 -1.260192e-01 -0.25406257 -0.154880107 -0.151754404
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP 0.2252138709 -0.016371911 0.37845026 -0.211838619 -0.067003022 -0.082541632 0.107463748 0.354471664 0.050713686 0.05482788 3.898683e-02 0.0381826905 -0.26206483 0.04681314 0.14091476 0.033986348 0.26834682 0.12993489 0.11032619 -0.004324969 0.16729155 -0.004938875 0.0658737109 -0.21012140 -0.044233735 -0.047256310 -0.15738147 -0.115751643 0.13986387 -0.054860717 -0.29955088 -0.13555352 -0.170517674 -1.622639e-01 -0.29957850 -0.092711253 0.087202988
LU_TUMOR_VASCULATURE_UP -0.2378969459 -0.062771846 -0.34031239 0.168539328 -0.005657595 0.008190157 -0.167323313 -0.338981975 -0.012484156 -0.02906254 7.237425e-02 -0.0041181720 0.05644821 -0.09547833 -0.17278295 -0.026587364 -0.15721892 -0.08290324 -0.07692133 0.027096635 -0.15539443 -0.039807725 -0.0907044859 0.15741811 0.099085419 -0.025321125 0.12258506 0.194526161 -0.21552019 0.417930079 0.09449431 0.15446705 0.179506032 2.947411e-01 0.20435875 0.153196747 -0.067708347
KORKOLA_EMBRYONAL_CARCINOMA_UP -0.0648890101 -0.032521742 -0.09549351 0.129393718 -0.193203052 0.019756674 0.033055489 0.012090742 0.162133586 0.15343460 5.965502e-02 -0.0946327900 -0.14723402 0.14926621 0.08055377 -0.069317678 0.09878785 0.05716404 0.27551849 0.032230796 -0.22770260 -0.151166173 -0.2096628767 -0.10471736 0.361843632 -0.171443414 -0.17937880 -0.066953233 0.01485418 0.028228846 -0.09265788 -0.07985186 -0.145152990 5.837802e-01 -0.10747460 -0.064683118 0.046388878
KORKOLA_TERATOMA_UP 0.0246879829 0.314207438 0.37605979 -0.179124841 -0.032379168 0.129238282 0.172225286 0.235548971 -0.014739292 0.16769097 1.663879e-01 0.0188106200 -0.04650602 0.01986651 0.08451226 -0.166920945 0.17295139 0.03802788 0.12813343 0.126220125 -0.18602937 -0.161481817 -0.1742658425 -0.24643129 -0.122836999 -0.327714071 -0.29192403 -0.145207142 -0.09418954 0.059783879 0.09598647 -0.03320679 0.003223224 -1.181121e-01 -0.17877126 0.090599349 0.095678786
KORKOLA_YOLK_SAC_TUMOR_UP -0.0007555054 -0.021421796 0.02632694 -0.035433567 0.141613226 0.019911372 -0.004796058 -0.001649931 -0.102005325 -0.05763990 3.689459e-05 0.1935898594 0.20317659 -0.19638421 -0.08784612 0.042714637 -0.07671928 0.02373285 -0.34386769 0.028515433 0.18531115 0.075685824 0.1123704848 0.11078104 -0.341628831 0.120190881 0.08150623 0.099416803 -0.10395047 -0.040783114 0.10255693 0.11340823 0.112870194 -6.356078e-01 0.19628606 0.082304700 -0.021816705
KORKOLA_CHORIOCARCINOMA_UP 0.1041128574 0.050802605 0.08356868 0.002616351 0.166705865 0.029083321 0.033339356 0.034863888 -0.145879153 -0.07857234 -1.949332e-02 0.1514434265 0.20246406 -0.23759405 -0.08452061 0.043151694 -0.08551227 -0.03830657 -0.31848162 0.011160018 0.16614410 0.086788071 0.0890085722 0.08732890 -0.362402733 0.121010372 0.11882511 0.112394298 -0.10527127 -0.045309504 0.09942631 0.07787554 0.114541375 -6.194077e-01 0.15411825 0.063366395 -0.063388257
KORKOLA_SEMINOMA_UP 0.0143883280 -0.061538315 -0.07332409 -0.002029272 0.217358315 0.098241098 0.032751796 -0.087814242 -0.081314491 -0.06460506 -5.616862e-03 0.1630969932 0.21820386 -0.21452236 -0.11089417 -0.032477859 -0.09300386 0.04122480 -0.28319229 0.073437921 0.09605443 0.020087468 0.1290883909 0.12890302 -0.381385908 0.084072436 0.16921641 0.055552661 -0.12958319 -0.053707297 0.10910509 0.13519677 0.161922009 -5.578087e-01 0.23735022 0.103641126 -0.056075120
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP 0.1123404419 -0.099246059 0.29251507 -0.325596653 -0.052662019 -0.012940114 0.154217301 0.308497258 0.189224705 0.17168566 1.231780e-01 0.1182710250 -0.19858688 0.12426680 0.23060251 -0.113059070 0.23861910 0.12627316 0.13843072 -0.039936738 0.03939179 -0.122691635 -0.0569411621 -0.14852082 -0.101765053 -0.037504955 -0.13765046 -0.140529751 0.04455761 -0.014788011 -0.25402909 -0.05853212 -0.116016632 -4.783914e-03 -0.41905900 -0.014673495 0.057442498
HOLLMAN_APOPTOSIS_VIA_CD40_UP -0.1151565209 0.052711436 -0.29807776 0.247422702 0.147590241 0.055423242 -0.142427543 -0.297218464 -0.186224424 -0.20741716 -1.121865e-01 -0.0760119941 0.24124543 -0.14203473 -0.20234670 0.043247386 -0.27180186 -0.07873619 -0.18050744 0.114991470 -0.02127029 0.167118090 0.0958585482 0.22051043 0.002936958 0.072780412 0.15534893 0.139476566 -0.15101819 -0.017452203 0.18358194 0.10429137 0.142368910 -3.065258e-02 0.33247353 0.112098951 -0.100935977
LIU_PROSTATE_CANCER_UP 0.2174486111 -0.073496729 0.28573856 -0.124499192 -0.057239993 -0.020429757 0.140693421 0.407214699 0.120220601 0.12989182 2.508589e-02 0.0967480905 -0.25967413 0.13919891 0.19209378 -0.031730039 0.24893454 0.09710975 0.17247772 -0.030756115 -0.11270677 -0.121554641 -0.0857006060 -0.09446246 0.010098924 -0.184232968 -0.21029038 -0.115727215 0.11745326 -0.045479539 -0.29983687 -0.12332926 -0.224404303 -3.488958e-05 -0.24405810 -0.081462154 0.140697510
LIU_SOX4_TARGETS_UP 0.0348520543 -0.161469634 0.26274156 -0.304202295 -0.050685124 -0.053041216 0.085962358 0.301189290 0.166324484 0.13116039 1.100475e-01 0.0647346500 -0.33897362 0.04852868 0.24684466 -0.016577714 0.23365434 0.07455878 0.16613184 -0.016965465 0.02436819 -0.227625669 -0.0004191321 -0.12194013 -0.111578239 -0.041314905 -0.09052165 -0.097587342 0.17721669 0.085952083 -0.28194043 -0.05932238 -0.057205746 5.321372e-02 -0.36367249 -0.015363998 0.142925944
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP -0.0934159787 0.060976175 -0.26757898 0.202795542 0.127852418 0.116405632 -0.105679519 -0.207537683 -0.127761790 -0.21806297 -8.009341e-02 -0.0570496808 0.35572293 -0.16622240 -0.23033722 -0.003656037 -0.24351471 -0.08281439 -0.21385192 0.089045910 0.05702248 0.162830271 0.1073197522 0.18581478 -0.043297663 0.140169126 0.16915870 0.130244227 -0.19356051 -0.078973917 0.21181563 0.09276215 0.124145090 -2.047438e-01 0.27452947 0.097684909 -0.088142625
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP -0.2531769445 -0.076391547 -0.35524046 0.178419647 -0.027932256 -0.062111318 -0.190294011 -0.401869438 -0.047034396 -0.09050315 -7.353341e-02 -0.0001531211 0.17442433 -0.05326287 -0.19853240 -0.023615069 -0.28054125 -0.06056164 -0.13689646 -0.006535930 -0.05171414 0.065779649 0.0174894144 0.18666747 0.145560303 0.080587372 0.12046867 0.174873906 -0.04655476 0.182351256 0.20782555 0.13377643 0.169157456 1.914065e-01 0.28928058 0.137016903 -0.018630858
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP -0.1411454025 0.047900582 -0.25625196 0.269176774 0.181462253 0.034784740 -0.116174263 -0.301870796 -0.044968652 -0.14811820 -8.208908e-02 -0.0352154619 0.29059194 -0.07287436 -0.20680686 0.017363938 -0.30032548 -0.11323896 -0.17005992 0.006601310 -0.06746557 0.077409057 0.0159590455 0.26558390 -0.037694782 0.167440913 0.21207543 0.140875368 -0.19160167 -0.060321378 0.24086742 0.10370036 0.094599476 2.850367e-02 0.28597165 0.029669499 -0.164314548
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP 0.1116529885 0.292188184 0.34831334 -0.123581722 0.050516147 0.145019714 0.206187041 0.163406743 0.007821523 -0.09940156 4.141215e-02 -0.0228886983 -0.05491470 -0.03095383 0.10860314 0.072183090 0.13099797 0.06711451 -0.07673696 0.041966891 0.25476428 0.177618166 -0.0154400900 -0.13870532 -0.100030138 -0.108760557 -0.10667785 -0.165118186 -0.21136962 -0.308830865 0.01307193 -0.01994302 -0.006007855 -5.126714e-01 0.03798671 -0.170143211 0.001351049
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP 0.2745402112 -0.044177556 0.31876654 -0.329339068 -0.105691495 -0.142140913 -0.003162191 0.157173800 0.089932849 0.07302904 -1.286126e-02 0.0758662612 -0.43830863 0.10777430 0.12826241 0.012040783 0.27425517 0.11749725 0.05930217 0.038952950 0.07519665 -0.100333208 0.0973981350 -0.10538721 -0.085077261 -0.021507687 -0.12994877 -0.094083007 0.20864101 -0.006430176 -0.19660903 -0.01719751 0.009752194 -1.663727e-01 -0.31852933 -0.004341272 0.203116535
FRASOR_TAMOXIFEN_RESPONSE_UP 0.2257957178 0.048434395 0.37131451 -0.247543764 -0.045657194 0.045635878 0.177470440 0.343445989 0.118508293 0.14408488 1.239577e-01 0.0438059242 -0.29647471 0.08855053 0.19195553 -0.026278996 0.24448407 0.11560848 0.07867322 -0.017378686 0.01098018 -0.168135671 -0.0825024498 -0.12893972 -0.172576527 -0.076678534 -0.18549006 -0.155205808 0.02425944 -0.011353726 -0.15818606 -0.07181830 -0.088612281 -2.797678e-02 -0.36273060 -0.104253429 0.030828162
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP -0.2233367530 -0.007741796 -0.37463807 0.260361044 0.062097031 0.042551473 -0.111730786 -0.361252426 -0.028706282 -0.04328331 -4.884767e-02 0.0149329143 0.25979025 -0.12316554 -0.20828246 -0.016039857 -0.15973390 -0.13573929 -0.06858283 0.107131118 -0.19184527 0.008118677 -0.0431836820 0.18748450 0.078381562 0.029201247 0.23179224 0.070307687 -0.20823179 0.030900475 0.23092058 0.16884357 0.117332432 1.166270e-01 0.32408086 0.047668182 -0.034181119
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP 0.1108356219 0.072625095 0.35562137 -0.266060947 -0.107490386 -0.048812016 0.183603465 0.203732983 0.195010034 0.30190337 5.026785e-02 0.1833451993 -0.21665967 0.10730554 0.19889431 -0.080954542 0.22126893 0.13154304 0.03614184 -0.220001339 0.11292678 -0.131457134 -0.0455743876 -0.27755754 -0.067880624 -0.016925423 -0.14254500 -0.174080097 0.03526815 -0.091897678 -0.03194165 0.07521659 -0.066452401 -4.426222e-02 -0.30126507 -0.155867534 -0.087824518
WATANABE_COLON_CANCER_MSI_VS_MSS_UP 0.1604393078 -0.046725031 0.24421714 -0.212744255 -0.088335734 -0.062050470 0.127640749 0.301282112 0.079637731 0.15503451 6.223935e-02 0.0203861980 -0.31159126 0.10664368 0.22892309 0.049192090 0.18292270 0.10162373 0.19409459 -0.004813772 -0.08510377 -0.099590371 -0.1592289695 -0.14987100 0.008425516 -0.293152578 -0.28643062 -0.040028563 0.18403042 0.088763148 -0.17183112 -0.07892018 -0.072561676 -5.959037e-03 -0.33781668 0.018589804 0.192669206
>
> proc.time()
user system elapsed
51.75 4.92 55.82
GSVA.Rcheck/tests/test_plage_newapi.Rout.save
R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> ## 2023-11-10 axel: simple test script for method PLAGE, new API
>
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
expand.grid, I, unname
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db
> library(GSVA)
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 1.4171739 -1.3444519 -0.99052898 0.4203395 1.30716224
g2 -0.7281951 0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754 0.09779699 -0.6792548 -0.09124045
g4 1.0735382 1.3156255 0.15588330 -1.8079608 0.48531108
g5 0.7229884 -0.9162342 1.93982245 0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> plagePar <- plageParam(X, gs)
> plage.es <- gsva(plagePar, verbose=FALSE)
> dim(plage.es)
[1] 100 30
> plage.es[seq.int(min(nRowsToPrint, nrow(plage.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 -0.029219588 0.134185958 0.3713074711 0.0407816079 0.06092767 -0.220481051 -0.263761945 0.150320487 -0.22409656 0.009584613 -0.39111762 -0.1302648585 -0.05959038 0.33696215 -0.07282788 0.073310843 0.05147115 -0.2483084427 -0.0858324287 0.178309261 0.38540679 0.046642663 0.122541902 0.015905580 -0.097924551 0.029203351 -0.06630956 -0.07126728 -0.194205126 0.14834577
gs2 0.009713309 -0.070894760 0.0887748898 0.0438945086 0.07597568 -0.099232840 0.257432656 -0.180783042 -0.26082831 -0.191077787 0.03035706 -0.1035337259 -0.19412605 -0.10714563 0.07146483 0.086637398 0.20308822 0.0140285507 -0.2137568863 0.239387383 -0.22371195 -0.206819710 -0.133382606 0.108114986 -0.046079067 0.089875594 0.42299690 0.41937892 0.096947556 -0.22669608
gs3 -0.139922266 -0.117741577 -0.0781834024 -0.2165908186 0.27378251 0.311048702 0.086846172 0.044475856 -0.08203218 0.119527132 0.03846745 -0.2109524281 0.12655940 -0.38507377 0.10369939 -0.017494211 0.16994906 -0.1420728947 -0.0785235706 0.004983979 -0.08761015 0.009889028 -0.094132008 -0.247835746 0.083711263 -0.250047995 -0.11800166 0.26164152 0.264615361 0.36701785
gs4 0.136784356 -0.055804012 -0.0003340026 -0.1516269802 -0.27114196 -0.083083560 -0.096565517 0.036868895 -0.06300502 -0.221561203 -0.19813522 0.1042473505 0.08093850 0.05674063 -0.19895817 0.067302708 0.25451893 -0.0005207089 -0.1159880895 0.048467793 -0.20603836 0.159545022 0.044036214 0.534771648 0.105886354 -0.017032347 0.07891909 -0.39111885 0.312125306 0.04976120
gs5 0.034934164 0.039749845 0.1228855856 -0.2732261283 0.04199286 0.103214014 -0.195436449 -0.287379571 0.03966687 0.303622722 0.07474143 0.0856083346 0.13595773 -0.01383837 0.35831980 -0.051209828 -0.43727399 0.1718981370 -0.1181945240 0.089941405 0.27917773 0.023292236 0.118740362 -0.297527028 -0.070561479 -0.048431187 0.02429263 -0.23305662 0.114527349 -0.13642802
gs6 -0.279844320 0.191897986 -0.3053996126 0.0094415284 0.04842640 0.194020478 0.096966418 -0.068898812 -0.20073135 0.378243740 -0.19309702 -0.1466213408 -0.14129713 -0.26167877 0.16969940 0.003873402 -0.06359659 0.1923023239 -0.2857295678 -0.037571361 -0.13741602 0.028278539 0.238658744 -0.074846882 0.198735207 0.142033651 0.30737897 -0.09691484 0.003752428 0.08993441
gs7 0.225539026 0.254315627 0.0211474628 0.3655580391 0.12888554 0.040475802 -0.108671963 -0.177723642 0.41116878 0.227671549 -0.28572797 -0.0471024585 -0.11298848 -0.14563561 -0.04101156 0.001529252 -0.30955146 0.2015628322 -0.0515248852 -0.202779772 0.26345240 -0.037525716 -0.006683093 0.089664221 -0.112755956 -0.152690537 -0.11819571 -0.06373540 -0.095213785 -0.16145252
gs8 -0.231283677 -0.053675557 0.0264131810 0.1359540470 0.08233788 -0.227928562 -0.087182432 -0.090687865 -0.08943693 0.307308887 -0.26623882 0.0138228392 0.21217554 -0.01320852 -0.37951349 -0.052096781 0.10783552 0.1598299126 -0.2189896514 -0.112309675 0.24977969 -0.065970466 0.140396761 0.076196677 -0.330320943 0.135782120 0.26952133 0.29550850 -0.055760954 0.06174143
gs9 -0.149696707 0.070112664 -0.3927757978 0.0404540759 0.05022070 0.286507502 -0.292734447 -0.111830390 0.01797344 -0.123194982 -0.12329977 -0.0405767884 0.05003308 0.38368419 0.01421485 0.062677869 -0.07909931 0.0486677864 0.0095880253 0.132223596 -0.28737944 0.178169340 -0.379773116 0.242912453 0.188194766 0.217203390 0.11001738 -0.02903181 -0.001529958 -0.09193259
gs10 -0.117672007 0.025542827 0.1308302520 -0.1626636222 -0.09699436 0.244461645 0.359249078 -0.191834856 0.03983472 0.146795086 0.06267437 -0.0434347372 -0.04176742 -0.06732570 0.13904093 -0.305077580 -0.02187673 0.1570480436 0.1334628532 -0.279021420 0.06938138 0.363531649 -0.201888466 0.258009015 0.084167939 -0.202884988 0.12079417 -0.11859744 -0.252643549 -0.23114107
gs11 -0.117405216 -0.048550062 -0.2152359244 0.1765495035 -0.15055137 -0.123720213 0.102298045 -0.027754231 0.20009873 0.250537460 -0.05653296 0.5188172981 -0.14533038 0.18956907 -0.05111332 -0.028603358 -0.08113559 -0.1326973408 -0.2163548884 0.153306782 -0.24927555 0.377259651 -0.143092985 -0.138807673 -0.201352437 -0.049677679 -0.09122352 0.11203847 0.069118818 0.11882086
gs12 -0.543671749 -0.184614928 0.1099977497 -0.0553393639 -0.40340420 0.033822756 0.082140727 0.090566044 0.06267315 -0.035981570 0.18191246 -0.1165185323 -0.14432586 0.18146646 0.03547440 0.236193030 0.02238259 0.0383756956 -0.0935119488 0.043760861 0.02041612 0.063399434 0.120073412 0.080158878 -0.122419354 0.011193111 0.21268970 -0.20265505 -0.123185463 0.39893143
gs13 -0.024887916 0.118584422 0.1388041889 -0.1413124768 -0.39825505 0.052045207 0.261267389 -0.255779352 0.08983137 0.244926313 0.25970077 -0.0188348892 -0.36760612 -0.01271960 -0.20002981 -0.087057056 -0.05944590 -0.1591285151 0.2077404356 0.302011283 -0.02371886 0.178685780 0.016103242 -0.065410956 0.141870716 -0.181431006 0.21774895 -0.11979818 0.016494216 -0.13039859
gs14 -0.100340055 0.077189402 0.0390858762 -0.0370017538 -0.38389060 0.184412799 -0.118805404 0.151984291 -0.25219352 -0.107177720 -0.13513101 0.0625168832 -0.10590181 -0.17815359 0.03224044 0.159411109 -0.08896745 -0.1280661493 0.1577303651 -0.038406698 -0.27702921 -0.122279723 0.239019808 0.128024840 0.212749941 0.142712690 0.18985273 -0.29773955 0.378010038 0.21614304
gs15 0.048774560 0.060119682 0.0484913743 0.2519843778 0.03039694 -0.234375681 -0.108291508 -0.453456336 0.06303550 0.086507823 -0.04349266 0.0260079589 -0.07031311 -0.07260948 0.19503960 0.264057607 0.30593891 0.1027550963 0.2715334959 -0.065807601 -0.15451764 0.253065015 -0.142033610 0.149114814 -0.156868088 -0.142545833 -0.28141243 -0.15529889 0.134277793 -0.21007769
gs16 -0.121838108 0.078038618 0.1774058118 0.3701311334 -0.27325953 0.179212470 -0.183228978 -0.297884469 0.07431105 0.142904264 -0.37912167 0.0392912596 0.31140398 -0.15567324 0.30015891 -0.075661103 -0.09261959 0.0039456916 -0.0540112724 -0.046884108 0.18371220 -0.073575237 0.236113549 0.114082325 -0.059486224 -0.043877650 0.05583114 -0.19847973 -0.131850692 -0.07909080
gs17 0.184799857 0.070052354 0.3514429664 0.1732326612 -0.22022967 0.003214861 -0.405239687 -0.047291743 -0.24679440 0.160056459 0.08518827 -0.0463285866 -0.06034854 -0.30001767 -0.19348991 -0.035213712 -0.09465668 0.0759894988 0.1785756235 -0.132155045 -0.17500659 0.376832927 0.013218793 0.018574170 -0.110793912 0.229997712 0.16584921 0.05705518 -0.156772307 0.08025791
gs18 -0.187087483 0.337139118 0.1688542303 0.1173035568 0.05984658 -0.185941480 -0.119363637 -0.382728482 -0.15395065 -0.319451357 -0.19733920 -0.0144161899 0.24873343 -0.10552473 0.04524322 -0.001873581 0.22373606 0.0229936448 -0.3542996024 0.061859205 0.02839072 0.078164766 0.344304336 0.045874812 0.009125945 0.025623338 0.17909395 0.09353534 -0.131011234 0.06316538
gs19 -0.059003209 -0.199168662 -0.1837419847 -0.2237610050 0.39738058 -0.326919064 0.087628623 0.181877873 0.35191549 -0.027680315 0.24795143 -0.1101431952 -0.01839169 -0.16235495 0.08701808 -0.090546490 0.16014091 0.1263778250 -0.0780805378 0.230737817 -0.22144812 -0.217901043 -0.019311240 -0.228211869 0.086283799 -0.067073673 0.17863523 -0.10809469 0.095046484 0.11083758
gs20 -0.087459182 -0.195412041 -0.0130357705 0.2848639974 0.22802341 -0.158851672 -0.203819293 -0.074651734 0.26441584 -0.163246538 -0.16645128 -0.0007860099 0.23034725 -0.10381161 -0.44439333 0.400370645 0.17176277 0.0072304296 -0.0820074325 0.083326015 -0.18145094 -0.041971647 0.076837721 0.000302442 0.174386727 -0.151895543 -0.01190509 0.10267278 -0.134531574 0.19114066
gs21 0.107602195 -0.142208461 -0.1560412602 0.1057618700 0.08242831 -0.094411152 -0.402862002 -0.372859070 0.03195170 -0.056225322 0.02369290 -0.0133280573 -0.19355100 -0.27795918 -0.03191200 0.364990768 0.28739587 0.1564537944 0.0719681085 0.169215470 0.29072561 -0.251367594 0.063227672 0.159273607 -0.096533492 0.163138228 0.01013211 -0.06972215 0.049191913 0.02183063
gs22 0.281156732 -0.185969190 0.1466983344 0.0988277638 -0.05639434 0.008345487 0.314359229 -0.035846835 -0.02674254 0.048462980 0.04194433 -0.2929134701 -0.02180503 0.16130641 -0.09628426 0.094556572 -0.17393215 -0.0501843811 0.0418822082 -0.042590804 0.17563655 -0.241418448 0.454068984 -0.195659705 -0.078786970 -0.020000914 -0.31312338 0.24019694 0.013901423 -0.28969152
gs23 0.287000160 -0.009577127 -0.0258026809 0.3978394227 0.06574872 0.165351593 0.202895394 -0.008028034 -0.07998444 0.210698794 0.07377611 -0.0586860376 -0.15454336 0.13418397 0.08296051 -0.055745695 -0.06072953 0.0004303990 -0.0731050722 -0.109362156 0.03413574 -0.043312239 -0.067080708 -0.310656179 -0.124265593 -0.262454623 -0.54504850 0.22851199 0.123089583 -0.01824042
gs24 0.226216800 -0.073685267 -0.0417664264 -0.0006964549 0.18170065 0.466969874 0.008804967 -0.038827882 0.15703216 -0.158480858 -0.21933991 -0.0418454781 0.08244118 0.05264244 0.19388981 0.261405034 -0.08604337 -0.2537728142 0.0002742249 0.022868190 -0.15317303 -0.197659709 0.102648478 0.127786731 -0.008318546 -0.272121666 0.17408086 0.09227398 -0.213205479 -0.39209848
gs25 -0.227611755 0.023775737 0.0723240408 -0.1495365735 0.06081540 -0.172945821 -0.104641914 -0.283228744 0.09443370 0.264032568 -0.30609675 0.1905985693 -0.15253022 0.33940139 0.05489225 0.083252511 0.19734533 -0.0236399481 0.2777489932 0.036835483 0.17108518 -0.190520756 0.150268031 -0.160683713 0.167731621 -0.006525896 0.10202510 0.02616628 -0.376857271 -0.15791283
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+ grep("^REACTOME", names(c2BroadSets)),
+ grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- plageParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+ minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.11442430 0.32079541 0.19023827 -0.16386259 -0.34124516 -0.08626990 0.006244354 -0.09133096 -0.07958067 -0.19080877 -0.129759539 -0.011392352 -0.053528324 0.137113192 0.122790549 0.185113826 0.255475291 0.289729331 -0.231805083 -0.10599439 -0.16563165 0.254730153 0.28736502 -0.07380857 -0.13262739 -0.00202695 -0.12848634 0.04738066 0.15451669 -0.042949836 -0.1917455098 -0.158789670 -0.030545427 0.1681240794 -0.02372029 -0.0981317670
KEGG_CITRATE_CYCLE_TCA_CYCLE -0.14376128 -0.40210177 -0.10732752 0.22556600 0.22044109 -0.04149364 0.082632466 -0.03088703 -0.10141600 0.21634351 -0.099937129 -0.238283100 0.059799913 -0.044056815 0.106146035 0.035855219 0.056963046 -0.091694988 -0.111915190 0.08270476 0.17136294 0.002778763 -0.17116078 0.04310892 0.38606731 0.26041385 0.18985748 -0.28660545 -0.22184771 -0.072806417 0.0353622058 0.097891536 -0.169106885 0.1413099205 -0.11591220 0.0357089449
KEGG_PENTOSE_PHOSPHATE_PATHWAY -0.16235500 -0.32582108 -0.11076423 0.23827639 0.33496725 0.02867445 0.017174780 0.06591909 0.10482653 0.18448109 0.051993550 -0.025185654 0.117266799 -0.086462365 -0.121860074 -0.309601472 -0.202595001 -0.203907440 0.166706699 0.13841854 0.05621760 -0.217255930 -0.23400863 0.03480311 0.03693621 0.18017005 0.17067361 -0.14698325 -0.15401687 -0.039631290 0.1852566211 0.251925461 0.059502652 -0.1710616230 -0.05714658 0.1444660100
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS -0.19045563 -0.30144436 -0.06208281 0.23907573 0.23514442 -0.11949500 0.256530147 -0.15784897 -0.07002696 0.18754970 -0.156566301 -0.233437891 -0.028875826 -0.135832499 0.007013319 -0.063573306 -0.045190431 -0.134951243 -0.119095747 0.08957830 0.20494217 0.014625096 -0.21685204 0.12579094 0.30068903 0.30284667 0.20017848 -0.22704585 -0.03911287 0.152821859 -0.0118501734 0.195309455 -0.129960080 0.0414442346 -0.05624288 -0.0535986719
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.08708061 0.36924639 0.16317478 -0.18733952 -0.22969884 -0.07403687 0.005513622 -0.13403336 -0.10757766 -0.11347043 -0.126968905 -0.068529526 -0.073097377 0.145409314 0.117559506 0.192280283 0.262745324 0.261030448 -0.187064190 -0.10806619 -0.21446933 0.264815017 0.32316348 -0.02316450 -0.08242710 0.09121413 -0.08115837 -0.06082489 0.05128248 -0.096144492 -0.1729482337 -0.179767986 0.079378632 0.2025544282 -0.14107384 -0.1545868541
KEGG_GALACTOSE_METABOLISM 0.13896759 0.33236986 0.15287628 -0.19570500 -0.37392490 0.03112239 -0.101122302 -0.02357435 0.03161318 -0.18551649 0.042859194 0.003683625 0.058836073 0.058593014 0.103013057 0.136717007 0.125649307 0.257519495 -0.059380958 -0.09369887 -0.16262023 0.145102780 0.38948984 -0.18103028 -0.24299641 -0.04474028 -0.20609816 0.05089387 0.23425714 -0.067198742 -0.1327201321 -0.208840024 -0.007338931 0.1015346567 0.02976531 -0.1383576213
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.08699846 0.02769904 0.03088309 -0.15783874 -0.16132270 0.07393045 -0.152562581 0.17928005 0.15457917 -0.11563182 0.248868576 0.203636007 0.038899707 0.177895808 -0.087598070 0.024330837 -0.068874923 0.166621148 0.195566178 -0.09919733 -0.51840256 -0.125338656 0.15816739 -0.06627634 -0.24722350 -0.12644374 -0.27029081 0.23656458 0.03682528 -0.172195675 0.1255991760 0.010036282 0.146200884 -0.1183297380 0.06921028 0.0957347869
KEGG_FATTY_ACID_METABOLISM 0.25246920 0.21487789 0.06756412 -0.24015561 -0.15971798 0.04164973 -0.134634522 0.18133621 0.18742246 -0.09879733 0.059789040 0.211657105 -0.189741758 0.051073442 -0.063493728 -0.055876110 -0.064518498 0.032865183 0.144745872 -0.12747677 -0.34740988 0.017286592 0.07659859 -0.12250954 -0.14145045 -0.32332540 -0.30311340 0.30156896 0.14235300 -0.020396100 0.1491018982 -0.054180990 0.209632783 -0.0622606872 0.15856855 0.0084981268
KEGG_STEROID_BIOSYNTHESIS -0.26848204 -0.15151075 0.27196342 0.20005723 0.05633948 0.06709033 -0.076856972 -0.08144521 -0.11182014 0.23060319 0.031572540 -0.043182612 0.162334518 -0.113794316 -0.221396081 0.039299968 0.198596097 -0.125931968 -0.101950870 0.12788728 0.03906626 0.135077658 -0.01696710 0.13279903 -0.12493729 0.40294067 0.30898303 -0.07471426 -0.07229951 -0.346954681 -0.0425758777 -0.008173547 -0.157861540 -0.0398692105 -0.24333940 0.0194526802
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 0.22788265 0.27727244 0.12605512 -0.15231262 -0.07420505 0.10099690 -0.110400990 0.02784962 0.28647176 -0.07980438 0.173249992 0.174422862 -0.001563672 -0.107332599 -0.175605638 -0.211736911 -0.291012627 0.054097637 0.082675881 -0.19222910 -0.13208641 0.074845949 0.13658238 -0.04373454 -0.29216427 -0.25438809 -0.14526442 0.35661858 0.13638691 0.113474381 -0.0882569668 -0.027551600 0.137701542 -0.1643334547 0.08505740 -0.0276586587
KEGG_STEROID_HORMONE_BIOSYNTHESIS 0.22975311 -0.04610095 0.10063919 0.12299358 0.03877036 0.13465162 0.088715672 0.03494038 0.14951930 -0.05843410 -0.117297356 0.306369502 0.111144794 -0.204491028 -0.060894682 -0.033714074 -0.112850883 0.124922513 -0.016199947 -0.31755512 -0.07037955 -0.124619972 0.26355333 -0.17914396 -0.22832643 -0.07349334 -0.47727891 0.09134310 0.19265056 0.233158643 -0.0247334479 0.032853743 0.146944492 -0.1899024173 -0.01884571 -0.0486620136
KEGG_OXIDATIVE_PHOSPHORYLATION 0.04757384 0.42969714 0.09223380 -0.31361918 -0.22482181 0.17872708 -0.156175716 0.03456549 0.07932693 -0.18222063 0.263950703 0.156720262 -0.054368092 0.125986316 0.006787002 -0.084583991 -0.046388261 0.156195922 0.171548956 -0.20861678 -0.19200932 -0.036138327 0.17882865 -0.06323935 -0.25938295 -0.15467774 -0.19415965 0.14534418 0.07217123 -0.002104513 -0.0639220237 -0.134737904 0.153885773 -0.0408505217 0.22491981 -0.1064463186
KEGG_PURINE_METABOLISM 0.20065318 0.29721544 0.19035916 -0.18768395 -0.14876802 0.07499662 -0.111130384 0.04279520 0.10058079 -0.18253753 0.104394237 0.237489023 -0.156272735 0.004695238 -0.018444109 0.010848786 -0.031681573 0.100509407 0.200116332 -0.20128343 -0.13295068 0.008116163 0.13517872 -0.16149991 -0.22650307 -0.34997849 -0.25612139 0.34931922 0.23373805 0.081067825 0.0055786780 -0.137452124 0.043582088 -0.1302252071 0.06943792 -0.0581394776
KEGG_PYRIMIDINE_METABOLISM 0.21386387 0.31876668 0.13823771 -0.14977881 -0.22350466 0.05640788 -0.109066678 0.08462733 0.05200829 -0.09300310 0.030350113 0.314550177 -0.257314444 0.018989332 0.005829506 0.037731104 0.070314765 0.162687671 0.059216742 -0.19130213 -0.19705259 0.038453179 0.10999248 -0.11951467 -0.20321833 -0.33534029 -0.21755611 0.34102133 0.23875776 0.060935006 -0.0074629043 -0.180715242 0.033546687 -0.0939514779 0.01458195 -0.0220880991
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM -0.20681031 -0.37748716 -0.12565805 0.26798513 0.26914186 -0.12685519 0.153416637 -0.01650182 -0.14404837 0.28618661 -0.253033160 -0.185735835 0.033980001 -0.059404347 -0.042798179 0.052827743 0.087918043 -0.047097005 0.002603537 0.12045456 0.02098204 -0.038730195 -0.18413718 0.08243411 0.13850374 0.35054894 0.23717572 -0.12482694 -0.12337093 -0.048174199 0.0483989160 0.232747019 -0.087796534 0.0098209646 -0.20356325 0.0009030612
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.01555983 0.39948710 0.26524975 -0.11344673 -0.30536311 0.13871948 -0.119877999 0.01826166 0.03199101 -0.13884023 0.000402732 0.228057870 -0.065492316 0.046027102 -0.120910813 -0.112044381 0.107682776 0.280525919 0.062717644 -0.08761679 -0.31120689 0.045531608 0.16292802 -0.12689384 -0.31176258 -0.11566649 -0.04943121 0.14634414 0.17297063 -0.064286408 -0.1019910400 -0.192809929 0.239116210 0.0222125604 -0.07591641 0.0297711570
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.14011533 0.44950137 0.13715860 -0.21286365 -0.25951992 0.03554671 -0.035671613 -0.01235037 0.10835898 -0.19692749 0.119707919 0.229911107 -0.124986706 0.071248763 -0.050382477 0.112207174 -0.038781286 0.141432934 0.158050492 -0.24246930 -0.20193494 0.019331667 0.10357964 -0.11758175 -0.13149796 -0.30066366 -0.23406437 0.28585381 0.13769399 0.074084706 0.0009278377 -0.149035605 0.067135796 -0.0470514419 0.08543382 -0.1214980980
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.18341492 0.34228948 0.05029107 -0.34818659 -0.10685182 0.09265336 -0.088466493 0.11016160 0.15517234 -0.26698602 0.224420582 0.146464701 -0.044408678 0.093719606 0.048431770 -0.038893096 -0.147876699 -0.001782784 0.121902396 -0.03997209 -0.15444379 -0.033776069 -0.00457758 -0.03957663 -0.17241854 -0.33220603 -0.31794663 0.27603631 0.13609807 0.092390238 0.0150196645 -0.116601679 0.108012207 -0.1542070774 0.21229246 0.0004075145
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS -0.14556385 -0.10361716 0.22024326 0.31503617 0.06126010 -0.11154855 0.086414704 0.09990315 -0.15911865 0.25419971 -0.371443880 0.088126533 -0.008249792 -0.058022569 -0.290894975 -0.038124927 0.289981591 0.243192257 -0.230345230 -0.15276445 -0.12892010 0.072417276 -0.01986629 0.04301764 -0.08484861 0.12551261 0.03154033 -0.09408278 -0.02997378 -0.054032625 0.0911418987 0.151438348 0.140147297 0.0839960430 -0.34942241 0.0332716988
KEGG_LYSINE_DEGRADATION -0.27646705 -0.27151298 -0.14559260 0.23343969 0.37761951 -0.14982544 0.071650219 -0.03606215 -0.11370614 0.13919560 -0.059279394 -0.148559519 -0.055897641 -0.004205009 -0.084549331 -0.125562528 -0.038538048 -0.095318136 -0.053812331 0.06965729 0.21281299 0.081810273 -0.18178297 0.22842373 0.26345436 0.22182994 0.31463356 -0.21013663 -0.18109835 -0.054938949 0.0360631509 0.177937829 -0.061732716 0.0873730291 -0.14374132 -0.0235819496
KEGG_ARGININE_AND_PROLINE_METABOLISM -0.16123111 -0.13057226 -0.11107844 0.02273494 0.21356398 -0.07436990 0.084384101 -0.16407155 -0.25289315 0.14391482 0.036172848 -0.326582857 0.055461961 0.147752762 0.096612753 -0.119843646 -0.098278801 -0.122948974 -0.211625005 0.19972609 0.33443209 0.139927393 -0.24553021 0.20165627 0.28074920 0.22470401 0.20124083 -0.21576039 -0.19741636 -0.022915154 -0.0511405637 0.032249241 -0.025522833 0.1225511902 -0.02111686 0.0150635951
KEGG_HISTIDINE_METABOLISM -0.38691525 -0.08953562 -0.10044464 -0.01426187 0.01496539 -0.13622135 0.073354885 -0.08532239 -0.06721292 -0.02768174 0.076490066 -0.047484587 0.166533226 0.046557442 0.088751653 0.005292349 -0.081057843 0.067987559 -0.094320047 0.21609906 0.44120825 -0.100792083 0.13452155 0.08461381 -0.02486270 0.31367516 0.26079310 -0.32426284 0.10030542 -0.211640562 -0.0433522226 0.176759090 -0.192709853 0.0459120461 -0.22119461 -0.0645469418
KEGG_TYROSINE_METABOLISM -0.32712829 -0.42822607 -0.12167600 0.02926148 0.09223972 -0.04442842 0.021231012 0.02765216 -0.03822786 0.04965165 0.123045871 -0.128743087 0.217063631 -0.020137764 -0.074664972 -0.110309150 0.009697748 -0.014759694 -0.068874216 0.21673625 0.25233361 -0.119479733 -0.10033969 0.17709985 0.13429743 0.33966951 0.19420105 -0.33874057 -0.09490785 -0.124655343 0.1026505643 0.260903234 -0.098142875 0.0001200643 -0.07224524 0.0778319820
KEGG_PHENYLALANINE_METABOLISM 0.40967474 0.19836523 0.08736858 0.02869842 -0.01374240 -0.09317232 0.234731915 -0.10208931 -0.02436911 -0.04192146 0.046894702 -0.010923766 0.047580560 0.042336433 0.092609398 -0.004019050 -0.309686433 -0.136083760 0.434626863 -0.10463787 -0.38590280 -0.094165597 0.21855328 -0.17952300 -0.11488955 -0.05718921 -0.22158783 -0.01384747 0.01198482 -0.007884161 -0.0977790774 0.182631715 0.047187141 0.0992475649 -0.03286374 -0.1362134528
KEGG_TRYPTOPHAN_METABOLISM 0.15935872 0.31858549 0.09156412 -0.23847420 -0.09302019 0.08275092 -0.025728297 0.07322292 0.19026430 -0.13868036 0.206619445 0.128988091 -0.078007790 0.096592856 0.011962634 -0.051351485 -0.180762468 0.061269834 0.238903090 -0.09208227 -0.10207168 -0.106243834 0.06774698 -0.08751554 -0.26540552 -0.25036631 -0.51241085 0.26365030 0.06499509 0.024424527 0.0203047444 -0.027556007 0.180543189 -0.0780303726 0.07999529 -0.0340353504
> pickrellPar <- plageParam(pickrellCountsArgonneCQNcommon_eset,
+ canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esrnaseq[seq.int(min(nRowsToPrint, nrow(esrnaseq))),])
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS -0.15214812 0.19079795 0.0106548721 -0.06539635 -0.11195287 -0.04362555 -0.31151529 -0.07757363 0.4492669 -0.18037776 0.04612305 -0.0300515212 0.0095461535 -0.17685565 0.0346814651 0.2305611 -0.0811595896 2.228039e-02 -0.0263523574 -0.003290343 -0.17154720 0.13948803 0.0247698576 0.13773137 0.13227548 0.14302214 -0.11441695 0.3020346 0.07079582 -0.052860583 -0.4212291 0.15020276 0.16979426 -0.1934081 0.003119229 -0.0533843888
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.15203505 -0.17111274 0.0192425535 0.05927134 0.10807196 0.11312140 0.28808722 0.12139802 -0.4880436 0.15299104 -0.04906447 -0.0147576258 0.0316875534 0.11937406 0.0089518864 -0.2637738 0.0406273352 -4.893202e-02 0.0399987391 0.020132090 0.24689245 -0.14284022 0.0008861416 -0.16483674 -0.08846222 -0.14421236 0.18663124 -0.3056940 -0.10053188 0.025582990 0.2761436 -0.11072658 -0.17974086 0.2615204 0.021548560 -0.0214665332
KEGG_PENTOSE_PHOSPHATE_PATHWAY -0.15765014 0.18674949 -0.0273930657 -0.07307133 -0.10533768 -0.09164663 -0.32248478 -0.11596237 0.4765833 -0.14616308 0.04285343 -0.0546959513 -0.0078616045 -0.15559699 0.0056289676 0.2402897 -0.0654167765 9.649199e-03 -0.0248954667 0.014836184 -0.19279004 0.15939724 0.0142917986 0.15493177 0.12077530 0.12820289 -0.13375282 0.3157634 0.06478541 -0.032853560 -0.3012578 0.15637181 0.18509625 -0.2567167 0.011332850 -0.0219922268
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS -0.09948024 0.17081884 0.0007132175 0.03385509 -0.06241216 -0.10503442 -0.20057306 -0.07219669 0.3963326 -0.12678766 0.06517810 0.0224058492 0.0671487290 -0.18608845 0.0013261299 0.2291769 -0.0210756261 2.665083e-02 -0.0991881059 -0.005604071 -0.49238630 0.15844499 0.0684573628 0.18159133 0.06988761 0.19261084 -0.14240752 0.2382392 0.02679420 -0.052668574 -0.3419867 0.13615421 0.10134608 -0.2093921 -0.007625566 0.0377750733
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.11684514 -0.15932375 0.0424584303 0.08863850 0.01606414 0.07687084 0.26942124 0.09040454 -0.4770715 0.19043992 -0.02814712 0.0084783419 0.0113907130 0.11293532 0.0081665138 -0.2110960 0.0520711362 5.324071e-05 0.0002572043 0.004341436 0.20787937 -0.14010382 -0.0237929613 -0.14074488 -0.11101353 -0.11615857 0.13347359 -0.3440427 -0.08201004 0.014824329 0.4008495 -0.13645213 -0.18798271 0.2656192 0.001164264 0.0452927563
KEGG_GALACTOSE_METABOLISM -0.10572541 0.20093414 -0.0337689448 -0.06828622 -0.05141289 -0.04603842 -0.27803249 -0.08715881 0.4593304 -0.16948100 0.02158359 -0.0228842754 -0.0251350377 -0.13562816 -0.0336397673 0.2240697 -0.0559377116 3.578987e-02 -0.0187799930 -0.009111103 -0.19168860 0.14544677 0.0582003469 0.14876379 0.04249027 0.08803668 -0.15131539 0.3368992 0.07977192 -0.004153293 -0.4096545 0.16989169 0.19432462 -0.2523470 0.001213619 -0.0565674873
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM -0.18741437 0.16387617 -0.0060310939 -0.03859070 -0.14802565 -0.06396724 -0.33253815 -0.09961008 0.4362764 -0.27301158 0.09626864 0.0270197462 0.0232057101 -0.31223804 0.0187798020 0.2361106 -0.0726098042 -4.028766e-03 -0.0969205827 0.054098119 -0.09624125 0.17262148 0.0381393930 0.13351280 0.05969382 0.20522582 -0.04629863 0.2630025 0.13133577 -0.077179005 -0.3109268 0.07680757 0.15756403 -0.1319563 0.004626489 -0.0005768344
KEGG_FATTY_ACID_METABOLISM 0.14404628 -0.17549826 -0.0168733006 0.03662427 0.13805007 0.13510632 0.29212490 0.11769787 -0.4538781 0.16997502 -0.05292794 -0.0171357447 0.0056091986 0.20068593 -0.0171192068 -0.2391582 0.0523800221 -3.355725e-02 -0.0037541309 0.007606301 0.26720390 -0.13680786 -0.0229006319 -0.12955701 -0.16649337 -0.18843753 0.11227260 -0.3030089 -0.07180728 0.065746889 0.3537898 -0.09725041 -0.16000999 0.1584219 0.002131614 0.0267022633
KEGG_STEROID_BIOSYNTHESIS -0.23993046 0.13867049 0.1187377626 0.05110320 -0.13720084 -0.17477296 -0.20358441 -0.12237759 0.4362713 -0.01023068 0.09255610 0.0831711016 -0.0316845885 -0.09055792 -0.0101667462 0.2066797 0.0664619590 6.476799e-02 0.0581287322 0.001741120 -0.22245981 0.14966908 -0.0538040397 0.16575480 -0.03806247 0.08839711 -0.09754098 0.3146994 0.09568740 -0.024727977 -0.3582404 0.08721987 0.08303645 -0.3500921 -0.182876427 0.0455568716
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS -0.10378950 0.13345241 0.0602863571 -0.16623904 -0.07063215 0.01365008 -0.19534754 -0.17435286 0.4708230 -0.07118342 0.11618557 -0.0502633451 -0.0554177755 -0.16614665 0.0076810221 0.2090015 0.0672454536 3.512318e-02 -0.0428960078 -0.024698829 -0.33368337 0.14917398 0.0139906079 0.08658955 0.10773984 0.14806389 -0.11894824 0.3430318 -0.01837218 -0.088410625 -0.4130314 0.11951559 0.13746845 -0.1309977 -0.048676576 0.0540649156
KEGG_STEROID_HORMONE_BIOSYNTHESIS -0.21197941 0.18630856 0.0301018384 -0.11630509 -0.04474517 -0.08691530 -0.11027761 -0.11733030 0.4409750 -0.20162476 0.13665328 0.0221236331 -0.0003285179 -0.14428211 0.0620844698 0.1180512 0.0562025241 1.740092e-01 -0.0893062456 0.018200638 -0.29453200 0.08782095 0.0795061796 0.14770804 -0.04685136 0.10482351 -0.13782587 0.3286641 -0.01216641 0.001473664 -0.4633424 0.07796440 0.16692838 -0.1512924 -0.030595788 0.0201011702
KEGG_OXIDATIVE_PHOSPHORYLATION 0.11392670 -0.15176080 -0.0078716193 0.03185503 0.08755261 0.16899727 0.27816007 0.10828366 -0.4984539 0.15443204 -0.05388480 -0.0005382922 0.0143975861 0.13323583 -0.0144179595 -0.1631206 -0.0012127107 -4.539461e-02 0.0435086752 0.022640863 0.29947218 -0.13776551 -0.0302126129 -0.18067891 -0.13765087 -0.16335643 0.12104839 -0.3312689 0.02163840 0.030604155 0.3449082 -0.11292053 -0.11048607 0.2310232 -0.025202957 -0.0394868208
KEGG_PURINE_METABOLISM 0.14576228 -0.17970119 0.0695643645 0.07390013 0.09426888 0.14811626 0.25313045 0.12971197 -0.4997313 0.16664358 -0.06909949 -0.0011720262 -0.0279803304 0.13994248 0.0019350762 -0.1746847 0.0245422008 -6.364770e-02 0.0941657279 0.013648424 0.26762396 -0.16851615 -0.0456918476 -0.19287243 -0.08967612 -0.14275219 0.16046531 -0.3211839 -0.02696631 0.051340413 0.2707759 -0.12761083 -0.17070100 0.2401788 -0.012335268 -0.0313934410
KEGG_PYRIMIDINE_METABOLISM -0.15527782 0.18681216 -0.0710134938 -0.09272258 -0.09107116 -0.15945406 -0.26422713 -0.13051958 0.4924685 -0.17590868 0.06869025 0.0017294883 0.0440173962 -0.15137425 -0.0069782437 0.1818896 -0.0252424604 5.910549e-02 -0.0641390004 -0.009211103 -0.25500824 0.17506163 0.0368705159 0.19122864 0.11892819 0.15054298 -0.17164591 0.3047345 0.02982096 -0.059310144 -0.2438609 0.10353402 0.16710577 -0.2540935 0.041640375 0.0268777463
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.16187518 -0.15242447 0.0445845851 0.03801959 0.16815027 0.15816036 0.18629258 0.13647099 -0.4547896 0.15764760 -0.09834758 -0.0673653703 -0.0327515803 0.13813612 -0.0001154741 -0.2242866 -0.0035237558 -8.144324e-02 0.0846143930 0.016951778 0.35755319 -0.12650621 -0.0869564600 -0.15472376 -0.13565892 -0.15047719 0.19304761 -0.2923463 -0.10340182 0.124156397 0.2929275 -0.08529239 -0.17347808 0.1458381 0.019564617 -0.0001020227
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.18425567 -0.21997777 0.0792549975 0.02796617 0.15066508 0.13108206 0.09096202 0.09603363 -0.4087696 0.19271142 -0.11346497 -0.0412294265 -0.0825276719 0.25407808 -0.0336109990 -0.1920607 -0.0511250493 -1.385250e-01 0.0965515196 -0.005825203 0.28983157 -0.12541010 -0.0631413865 -0.18063408 0.07210946 -0.15207612 0.12502562 -0.3434555 -0.08266163 0.241050135 0.2367705 -0.13650734 -0.16052837 0.1219852 0.122337569 0.0188602175
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.21582742 -0.19257267 0.0481026570 0.12532384 0.12863263 0.12702487 0.21916790 0.14145654 -0.4628510 0.18903573 -0.08990904 -0.0356654022 -0.0293211714 0.21616290 0.0113339421 -0.2359683 0.0240081539 -8.452455e-02 0.0615230196 -0.031731840 0.26949610 -0.14960573 -0.0490440852 -0.18626782 -0.06807870 -0.13588057 0.13260775 -0.3153507 -0.07004173 0.095123437 0.2314867 -0.12190522 -0.17317799 0.1942247 0.001740289 -0.0003819966
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION -0.13320980 0.19146649 0.0001692046 -0.04724794 -0.11203115 -0.10900765 -0.32384751 -0.08670029 0.4661106 -0.15194445 0.02163166 0.0263972205 -0.0156839833 -0.23372426 0.0016790308 0.2330446 -0.0339518900 2.867854e-02 -0.0347112069 -0.013832614 -0.26086893 0.15508615 0.0463970898 0.12786410 0.13562535 0.16840661 -0.11800503 0.3056234 0.08931534 -0.062290601 -0.3304639 0.11023004 0.15287141 -0.1761863 -0.010338119 -0.0065512747
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS -0.18497233 0.17649821 0.0506236410 -0.08746720 -0.15678895 -0.18326441 -0.19998683 -0.08831954 0.4498416 -0.09855080 0.04904952 0.0387063020 0.0391040897 -0.19473731 -0.0088725559 0.2294151 -0.0153974275 8.110413e-02 -0.0361551097 -0.038686397 -0.29902619 0.15638790 0.0813030069 0.15365219 0.07778971 0.14702327 -0.22562370 0.2961998 0.06095390 -0.060339944 -0.3294075 0.14871582 0.15615268 -0.1661644 -0.018031872 -0.0007282847
KEGG_LYSINE_DEGRADATION -0.14840078 0.19887266 -0.0896794806 -0.05874662 -0.09522200 -0.16067588 -0.25024857 -0.12714531 0.5089357 -0.17188541 0.06501566 0.0211715670 -0.0087000106 -0.11468731 -0.0192207645 0.1887464 -0.0086852919 9.220565e-02 -0.0997662839 -0.015545295 -0.25889646 0.14938001 0.0102360429 0.15953226 0.08245914 0.11756512 -0.12447080 0.3428059 0.05803155 -0.041416622 -0.2706288 0.11974209 0.19925355 -0.2252852 -0.018670642 -0.0059757956
KEGG_ARGININE_AND_PROLINE_METABOLISM -0.15599441 0.17162854 -0.0165755907 -0.04984281 -0.13252570 -0.13503025 -0.24149898 -0.12496608 0.4652361 -0.18264708 0.06245441 0.0533993450 0.0200002688 -0.17588537 0.0187300201 0.2268855 -0.0308582433 6.457058e-02 -0.0409831672 -0.022302704 -0.26703092 0.13286020 0.0597241639 0.15221801 0.12299299 0.13822870 -0.16751098 0.3220956 0.08792924 -0.097087427 -0.3352892 0.08674901 0.18213748 -0.1854224 -0.015128027 0.0087392720
KEGG_HISTIDINE_METABOLISM -0.16341627 0.21211137 -0.0597047650 -0.07019812 -0.06569836 -0.16907760 -0.24238369 -0.09397806 0.4720904 -0.22248144 0.09449529 0.0337872241 0.0814929382 -0.14765066 0.0166344423 0.1896539 -0.0151032687 7.080535e-02 -0.0387446192 -0.034208862 -0.28356932 0.13501819 0.0592272252 0.14530433 0.09060491 0.16483382 -0.08830364 0.3105553 0.03130984 -0.076375024 -0.3379780 0.10320490 0.12281655 -0.2312373 -0.020753794 0.0269168631
KEGG_TYROSINE_METABOLISM -0.10093863 0.18267763 -0.0242538303 -0.06443060 -0.02632197 -0.16928691 -0.21835995 -0.12802624 0.4897721 -0.20718144 0.08915284 0.0230208339 0.0685731978 -0.11497401 0.0264683523 0.1715784 -0.0240623350 5.461238e-02 -0.0359349395 -0.041186627 -0.34571344 0.11565207 0.0429404806 0.15350966 0.12352853 0.16156040 -0.14241499 0.3437890 -0.02098569 -0.034677062 -0.3320536 0.12420589 0.08212171 -0.1959923 -0.039814920 0.0134459864
KEGG_PHENYLALANINE_METABOLISM -0.13596282 0.06742145 0.0882449903 -0.02244406 -0.09867622 -0.06439912 -0.08447981 -0.15306648 0.4203738 -0.10031185 0.17368849 0.0780588540 0.0996577430 -0.02544390 0.0171562407 0.1211227 0.0235791297 8.347408e-02 -0.2466780511 -0.006247915 -0.61710863 0.07252436 0.0317753835 0.10302349 0.06683344 0.11139551 -0.15093291 0.2664307 0.04334024 -0.011422551 -0.1744265 0.11107338 0.02648540 -0.2152238 0.019167613 0.0819975622
KEGG_TRYPTOPHAN_METABOLISM 0.17049240 -0.19170650 0.0004630847 0.05089247 0.12593277 0.11515466 0.27670376 0.12909756 -0.4814202 0.17977370 -0.06320424 -0.0194461931 0.0070929693 0.19100894 -0.0230060896 -0.2042648 -0.0001048516 -7.878183e-02 0.0931404987 -0.026808640 0.24465868 -0.13838085 -0.0248749524 -0.16243909 -0.09741608 -0.15878157 0.07600539 -0.2897865 -0.09352519 0.056621625 0.3530154 -0.08401918 -0.15938269 0.2105366 0.043211634 -0.0264526019
>
> gbmPar <- plageParam(gbm_eset, brainTxDbSets)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up 0.009503434 -0.07148275 0.03702570 -0.1449671 -0.06040476 -0.07594821 -0.08471232 -0.011938741 0.02993423 0.065023141 0.01762836 -0.11912551 -0.05949992 0.00525537 -0.05523948 -0.05372246 -0.08443369 -0.08598174 -0.11875051 -0.042058976 -0.04030687 -0.085476621 -0.10685594 0.02611153 0.04356317 -0.0705649980 -0.006844708 -0.01728745 -0.05473265 -0.02670516 -0.023271397 0.028072017 -0.03921781 -0.10235048 -0.05010187 -0.07005158 -0.09209016 -0.10881587 -0.05062336 -0.007877207 -0.08243841 -0.06962198 -0.08767648 -0.02583498 -0.04666987 -0.07810986 -0.01152421 0.02981450 -0.08655273 -0.024763415
astroglia_up 0.047878697 0.13259958 0.09353196 0.1723954 0.05397369 0.09437815 0.12333017 0.034441261 -0.02691552 0.082648790 0.05525398 0.07854437 0.02675066 0.14436470 0.03635936 0.07445693 0.18500914 0.12978579 0.10685532 -0.046038185 0.03640657 0.134998687 0.14571431 0.16997016 0.02481540 0.0363660300 -0.020974725 0.08501924 0.13807016 0.11677809 -0.008999474 -0.020349973 0.05204384 0.04461865 0.09432334 0.05564952 0.05441292 0.07187041 0.06496384 -0.016408375 0.06458610 0.08187014 0.14767961 -0.01197801 0.03687600 0.06445718 0.01797752 0.01595298 0.09244863 0.052499964
neuronal_up -0.109710924 -0.01702066 0.01301810 -0.0150155 -0.09724660 0.02146057 0.05010519 -0.040146081 -0.06066290 -0.006770987 -0.11536936 0.07187279 0.06404673 0.05934842 0.01706701 0.06703005 -0.05028874 0.06844218 0.03520158 -0.007305407 -0.02100709 -0.009551983 -0.02286479 0.02104686 0.02714991 0.0009992218 -0.091286596 0.04988690 0.05224805 0.04092799 -0.012195643 0.009698397 -0.03329177 -0.03730078 -0.06501777 0.00777109 -0.01276343 -0.07101898 -0.03167425 0.008950496 -0.04525475 0.03152291 -0.05007149 -0.06206634 0.00277177 0.05362907 0.06015409 -0.12476908 0.01965553 -0.006541254
oligodendrocytic_up -0.053316262 -0.03076570 -0.13026183 -0.1054244 -0.15884604 -0.04584733 0.01162552 -0.008735686 -0.07831724 0.029790216 -0.12264757 -0.17633055 -0.22829418 -0.09563053 0.01913198 -0.08062237 0.06710752 -0.04973426 -0.09459566 -0.035043759 -0.07087794 -0.024834220 -0.14132943 -0.08015759 -0.12351419 -0.1018570138 -0.145485987 -0.08031675 -0.13791221 -0.06314112 -0.055013638 -0.111969729 -0.06278656 -0.12395121 -0.11149668 -0.13560637 -0.03100847 -0.11540779 -0.19569986 -0.004032233 -0.09848717 -0.01310448 -0.01601479 -0.08806238 -0.15998008 -0.03256551 -0.02666356 -0.04873438 -0.04271502 -0.015764935
TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up -0.10887523 -0.07864038 -0.04197239 0.095668384 0.18776408 0.25307779 0.08792407 0.05994647 0.13261591 0.021215334 0.1151069 0.12610727 0.11787216 0.03692715 0.07098464 0.06193001 0.05640898 0.07437529 0.03446988 0.13673871 0.05740561 0.04951662 -0.03940410 0.07655210 0.08887779 0.06360155 0.063447530 0.09165828 0.10386274 0.098671883 0.08994742 0.14845583 0.05137301 0.101763991 0.0439691905 0.12523626 -0.05949182 -0.02266147 0.04146871 -0.01734481 0.02456185 -0.005848951 0.11898178 -0.003748745 0.04014935 0.049498323 0.0378446673 0.028926994 0.081286268 0.06431596
astroglia_up 0.13560615 0.06372746 0.09853784 -0.061051452 0.01577089 -0.04760733 -0.01301234 -0.02033879 0.03042881 0.007860558 0.1302317 0.04866147 0.11807311 0.02651416 -0.02576869 -0.02249800 0.03139450 0.01262743 0.10298674 0.04376961 -0.02441912 0.04007613 0.10426429 0.05984316 0.09531040 0.01361742 -0.006054302 0.01417130 0.01785855 -0.024485729 0.04885270 0.04978712 0.01089287 -0.003688539 -0.0255875216 -0.05318817 0.01572855 -0.04017804 -0.01581070 0.08027547 0.06475093 -0.019267885 -0.01000033 -0.012468882 0.03808888 0.016444129 0.0004891894 0.006058522 0.001277776 0.04623002
neuronal_up -0.01603674 0.03026768 -0.04846411 -0.081274578 0.03036729 -0.10588657 -0.04819897 -0.21472580 -0.07924660 -0.014852256 -0.3937604 -0.10090691 -0.42227945 -0.02226663 -0.03522747 -0.15937196 0.02880150 -0.03360695 -0.19537945 -0.02678998 -0.01237703 -0.05800257 -0.08946093 0.02804959 -0.33447989 -0.06646701 0.001490673 -0.06111592 -0.00788255 -0.005433944 0.08875419 -0.04552211 0.06832540 -0.054242676 -0.0165587308 0.03709143 0.08683758 0.07694510 0.00983925 0.05086959 0.03951686 0.046397028 0.03379387 0.065956603 0.07285765 0.002567756 0.0022974121 0.076873274 0.040563891 -0.04577361
oligodendrocytic_up -0.09082646 -0.03209598 -0.06775336 -0.001343057 0.09570037 -0.04469363 -0.03506036 -0.09033811 0.01079102 -0.008493560 -0.1060987 0.02222565 -0.09131953 -0.02902642 -0.01525947 -0.07435504 0.08049313 0.05654690 0.03601434 0.01580467 -0.08981765 -0.01162585 0.03884722 -0.00640505 -0.11088869 0.06651459 0.048149691 0.05667692 0.06740432 0.057691526 0.05627159 0.01676310 0.06553035 0.068221314 0.0005776113 -0.02757186 0.07961760 0.03639202 0.08426877 0.07545897 0.07456736 0.040406936 0.06787397 0.080378144 0.05427988 0.059627054 0.0040825991 0.039001591 0.038807887 0.01393330
TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up 0.10254985 0.1209366458 0.005457102 0.05470414 0.05324132 0.004583494 0.07287897 0.01803334 0.092298928 0.106581126 0.03911847 0.08760433 0.08083304 0.12273304 0.08658859 0.09439140 0.12859993 0.12899656 -0.05799326 0.043791271 -0.12734557 -0.07620178 -0.101627927 0.07398850 -0.14128439 0.04168816 -0.10586947 -0.07738761 -0.05189054 -0.04129260 -0.029881354 -0.02425999 -0.03083819 -0.01363261 -0.03413866 0.03369514 -0.02533095 -0.026089207 -0.05887989 -0.023565388 -0.02660048 -0.13175535 -0.131223466 -0.04934655 -0.07222247 0.04595771 -0.002484733 -0.02006267 -0.02129216 0.0121870804
astroglia_up 0.01473182 -0.0002823507 -0.041514372 -0.04221281 0.05781689 0.010362305 -0.03948686 -0.02292038 0.009218869 0.003819796 0.08805820 0.05787047 -0.04832227 -0.04771188 -0.03770525 -0.00397720 0.01702062 -0.04901255 -0.15053965 -0.066808334 -0.12029138 -0.13543562 -0.111383004 -0.11055588 -0.07080332 -0.05626645 -0.16040451 -0.06003255 -0.11320734 -0.07762499 -0.067457036 -0.06885981 -0.07206253 -0.09501078 -0.08210609 -0.14076913 -0.09259525 0.017705647 -0.07440865 -0.075879552 -0.10686648 -0.12383580 -0.109491916 -0.05092156 -0.12756381 -0.04676953 0.016467894 -0.08296504 -0.11449864 -0.0624475003
neuronal_up -0.05510838 0.0693924418 0.049907805 0.06579639 -0.03553495 0.060569667 0.04258533 0.05347991 0.011061722 -0.022561037 0.05657129 0.08324986 -0.06484210 0.05410708 0.08696189 0.04328396 0.04756120 0.05241028 0.03859840 0.004121992 0.05429824 0.06696186 0.039995573 -0.03731216 0.03871302 0.01346663 -0.02003846 0.03361013 0.08956373 0.05912840 0.004434217 -0.12181570 0.03493980 0.01353410 0.04421769 0.01083988 0.03740344 -0.008455138 0.03989240 0.043233261 0.03530835 0.04811405 0.067893057 0.06035066 0.05073357 0.04311893 0.074185702 0.05368352 0.04001603 -0.0368438811
oligodendrocytic_up 0.01488734 0.0588328752 0.073964840 0.05639762 0.06448371 0.103919757 0.05028910 0.07722783 0.094043741 0.035205083 0.07003096 0.06202171 0.04362975 0.05582357 0.08811635 0.07662414 0.06354034 -0.13317556 0.09801811 0.010237076 0.04782735 0.09917287 0.003572068 0.02818885 0.12062411 0.06959310 0.09380954 0.09824244 0.04046508 0.05673212 -0.016644605 -0.11809801 0.06714657 0.02817944 0.07503049 -0.01017455 -0.01208933 -0.031760653 -0.16273288 0.008979194 0.06577860 0.08468706 0.006857635 -0.03150528 -0.03036885 0.08254308 0.070749406 0.09400074 -0.01657986 -0.0003181655
TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up -0.12793182 0.05813961 -0.02996638 -0.03999179 -0.01317216 -0.06556770 -0.06014645 -0.10524550 0.03410507 0.03174620 -0.07131517 -0.03864651 -0.00656357 0.004862977 -0.05760770 -0.03220225 -0.14379979 0.006209294 0.01015281 -0.02506194 -0.15712941 -0.06978470 -0.039842096
astroglia_up -0.07509997 -0.03112873 -0.07460949 -0.10572792 -0.07367029 -0.08467325 -0.05192066 -0.04367356 -0.07272862 -0.06252615 -0.10738803 -0.07352765 -0.08211912 -0.086061829 -0.11834540 -0.05541622 -0.05335162 -0.071461495 -0.06913880 -0.14663735 -0.10229018 -0.04606975 -0.030543430
neuronal_up 0.04965757 0.03625217 0.04174849 0.04119978 0.04325152 0.04343971 0.04604542 0.03545067 0.04582293 0.07345420 0.01598958 -0.00251816 0.03897229 -0.071738618 0.06571136 -0.05706466 0.03314141 -0.016854947 0.07308937 0.04576623 0.03139639 0.06476292 0.047577132
oligodendrocytic_up 0.06265322 -0.03057294 0.08799201 0.04420027 0.07389345 0.10096870 0.02276466 0.04904987 0.08861485 0.09026904 0.06005119 0.02120084 -0.02586168 0.056221418 0.04705479 0.02053537 0.11599128 0.059425833 0.04519846 0.09306496 0.10243557 0.07848995 0.009634767
>
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> leukPar <- plageParam(leukemia_eset, cgpC2BroadSets,
+ minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP -0.1733940255 -0.033909950 -0.21494771 0.225895163 0.063750234 0.167895761 -0.120141623 -0.301364574 -0.127897961 -0.17662816 -2.033307e-03 -0.0580768131 0.22143221 -0.10332109 -0.22150927 0.043353690 -0.25639842 -0.09207537 -0.08853224 0.026931498 -0.14639547 0.099528895 -0.0728970131 0.20132393 0.071949059 0.065447939 0.14428259 0.131615034 -0.13550381 0.058275958 0.32869002 0.11720023 0.110313219 1.576915e-01 0.36374728 -0.052301552 -0.221995813
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP 0.0091056904 -0.007229294 -0.26682324 0.239296160 0.102079970 0.107282626 -0.220934366 -0.114993916 -0.242707246 -0.35282402 -1.319142e-01 -0.2908596517 0.19217905 -0.05096841 -0.30028124 0.081213713 -0.06235553 -0.03413274 0.14630064 0.233615255 -0.02563993 0.216233541 0.1512191200 0.18209821 0.096718310 0.012136911 0.05625600 0.144054943 0.15035428 -0.046779826 -0.05975187 -0.23316425 -0.056470909 -4.192709e-02 0.16251868 0.109530419 0.147564140
WINTER_HYPOXIA_UP 0.0834055313 -0.070653851 0.36411795 -0.247095973 -0.178229854 -0.221082475 -0.024371138 0.180921942 0.038462365 0.10271188 -6.399298e-02 -0.0082717873 -0.01821576 0.28000441 0.17834176 -0.050337001 0.11095592 0.07805238 0.10651755 -0.242836351 0.23470420 0.062017426 0.0444107834 -0.26140415 0.191019536 0.057727131 -0.25471951 0.003543483 0.20328048 0.027252717 -0.16090502 -0.15356573 -0.065566664 5.311727e-02 -0.35349585 -0.060628683 0.034808040
PYEON_HPV_POSITIVE_TUMORS_UP -0.1194662949 0.038017996 -0.28521866 0.275081686 -0.031488732 -0.038588970 -0.100533814 -0.297050611 -0.238634457 -0.29082863 -7.600985e-02 -0.2335338233 0.31515092 -0.08353618 -0.18336902 0.087151767 -0.20372452 -0.14291385 0.03273765 0.233092544 -0.04825298 0.113859039 0.0442618489 0.16991714 0.231386554 0.005267212 0.03397312 0.099018174 -0.04752945 0.167145951 0.12918791 -0.11535230 0.055991634 8.848689e-02 0.24812128 0.117475851 0.050707009
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP 0.1198739462 0.187824071 0.39422522 -0.345600421 -0.152731606 -0.106308076 0.142740956 0.120710037 0.111680385 0.07724317 -8.733673e-03 0.0899926339 -0.06187972 0.35041893 0.14911728 -0.027779682 0.08478613 0.05561965 0.01558144 -0.248802758 0.23046261 0.041120203 -0.0006047729 -0.26801992 -0.003634823 0.026561742 -0.21188895 -0.043144995 0.07637875 -0.133457745 0.15331729 -0.05186474 -0.076486263 -1.260192e-01 -0.25406257 -0.154880107 -0.151754404
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP 0.2252138709 -0.016371911 0.37845026 -0.211838619 -0.067003022 -0.082541632 0.107463748 0.354471664 0.050713686 0.05482788 3.898683e-02 0.0381826905 -0.26206483 0.04681314 0.14091476 0.033986348 0.26834682 0.12993489 0.11032619 -0.004324969 0.16729155 -0.004938875 0.0658737109 -0.21012140 -0.044233735 -0.047256310 -0.15738147 -0.115751643 0.13986387 -0.054860717 -0.29955088 -0.13555352 -0.170517674 -1.622639e-01 -0.29957850 -0.092711253 0.087202988
LU_TUMOR_VASCULATURE_UP -0.2378969459 -0.062771846 -0.34031239 0.168539328 -0.005657595 0.008190157 -0.167323313 -0.338981975 -0.012484156 -0.02906254 7.237425e-02 -0.0041181720 0.05644821 -0.09547833 -0.17278295 -0.026587364 -0.15721892 -0.08290324 -0.07692133 0.027096635 -0.15539443 -0.039807725 -0.0907044859 0.15741811 0.099085419 -0.025321125 0.12258506 0.194526161 -0.21552019 0.417930079 0.09449431 0.15446705 0.179506032 2.947411e-01 0.20435875 0.153196747 -0.067708347
KORKOLA_EMBRYONAL_CARCINOMA_UP -0.0648890101 -0.032521742 -0.09549351 0.129393718 -0.193203052 0.019756674 0.033055489 0.012090742 0.162133586 0.15343460 5.965502e-02 -0.0946327900 -0.14723402 0.14926621 0.08055377 -0.069317678 0.09878785 0.05716404 0.27551849 0.032230796 -0.22770260 -0.151166173 -0.2096628767 -0.10471736 0.361843632 -0.171443414 -0.17937880 -0.066953233 0.01485418 0.028228846 -0.09265788 -0.07985186 -0.145152990 5.837802e-01 -0.10747460 -0.064683118 0.046388878
KORKOLA_TERATOMA_UP 0.0246879829 0.314207438 0.37605979 -0.179124841 -0.032379168 0.129238282 0.172225286 0.235548971 -0.014739292 0.16769097 1.663879e-01 0.0188106200 -0.04650602 0.01986651 0.08451226 -0.166920945 0.17295139 0.03802788 0.12813343 0.126220125 -0.18602937 -0.161481817 -0.1742658425 -0.24643129 -0.122836999 -0.327714071 -0.29192403 -0.145207142 -0.09418954 0.059783879 0.09598647 -0.03320679 0.003223224 -1.181121e-01 -0.17877126 0.090599349 0.095678786
KORKOLA_YOLK_SAC_TUMOR_UP -0.0007555054 -0.021421796 0.02632694 -0.035433567 0.141613226 0.019911372 -0.004796058 -0.001649931 -0.102005325 -0.05763990 3.689459e-05 0.1935898594 0.20317659 -0.19638421 -0.08784612 0.042714637 -0.07671928 0.02373285 -0.34386769 0.028515433 0.18531115 0.075685824 0.1123704848 0.11078104 -0.341628831 0.120190881 0.08150623 0.099416803 -0.10395047 -0.040783114 0.10255693 0.11340823 0.112870194 -6.356078e-01 0.19628606 0.082304700 -0.021816705
KORKOLA_CHORIOCARCINOMA_UP 0.1041128574 0.050802605 0.08356868 0.002616351 0.166705865 0.029083321 0.033339356 0.034863888 -0.145879153 -0.07857234 -1.949332e-02 0.1514434265 0.20246406 -0.23759405 -0.08452061 0.043151694 -0.08551227 -0.03830657 -0.31848162 0.011160018 0.16614410 0.086788071 0.0890085722 0.08732890 -0.362402733 0.121010372 0.11882511 0.112394298 -0.10527127 -0.045309504 0.09942631 0.07787554 0.114541375 -6.194077e-01 0.15411825 0.063366395 -0.063388257
KORKOLA_SEMINOMA_UP 0.0143883280 -0.061538315 -0.07332409 -0.002029272 0.217358315 0.098241098 0.032751796 -0.087814242 -0.081314491 -0.06460506 -5.616862e-03 0.1630969932 0.21820386 -0.21452236 -0.11089417 -0.032477859 -0.09300386 0.04122480 -0.28319229 0.073437921 0.09605443 0.020087468 0.1290883909 0.12890302 -0.381385908 0.084072436 0.16921641 0.055552661 -0.12958319 -0.053707297 0.10910509 0.13519677 0.161922009 -5.578087e-01 0.23735022 0.103641126 -0.056075120
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP 0.1123404419 -0.099246059 0.29251507 -0.325596653 -0.052662019 -0.012940114 0.154217301 0.308497258 0.189224705 0.17168566 1.231780e-01 0.1182710250 -0.19858688 0.12426680 0.23060251 -0.113059070 0.23861910 0.12627316 0.13843072 -0.039936738 0.03939179 -0.122691635 -0.0569411621 -0.14852082 -0.101765053 -0.037504955 -0.13765046 -0.140529751 0.04455761 -0.014788011 -0.25402909 -0.05853212 -0.116016632 -4.783914e-03 -0.41905900 -0.014673495 0.057442498
HOLLMAN_APOPTOSIS_VIA_CD40_UP -0.1151565209 0.052711436 -0.29807776 0.247422702 0.147590241 0.055423242 -0.142427543 -0.297218464 -0.186224424 -0.20741716 -1.121865e-01 -0.0760119941 0.24124543 -0.14203473 -0.20234670 0.043247386 -0.27180186 -0.07873619 -0.18050744 0.114991470 -0.02127029 0.167118090 0.0958585482 0.22051043 0.002936958 0.072780412 0.15534893 0.139476566 -0.15101819 -0.017452203 0.18358194 0.10429137 0.142368910 -3.065258e-02 0.33247353 0.112098951 -0.100935977
LIU_PROSTATE_CANCER_UP 0.2174486111 -0.073496729 0.28573856 -0.124499192 -0.057239993 -0.020429757 0.140693421 0.407214699 0.120220601 0.12989182 2.508589e-02 0.0967480905 -0.25967413 0.13919891 0.19209378 -0.031730039 0.24893454 0.09710975 0.17247772 -0.030756115 -0.11270677 -0.121554641 -0.0857006060 -0.09446246 0.010098924 -0.184232968 -0.21029038 -0.115727215 0.11745326 -0.045479539 -0.29983687 -0.12332926 -0.224404303 -3.488958e-05 -0.24405810 -0.081462154 0.140697510
LIU_SOX4_TARGETS_UP 0.0348520543 -0.161469634 0.26274156 -0.304202295 -0.050685124 -0.053041216 0.085962358 0.301189290 0.166324484 0.13116039 1.100475e-01 0.0647346500 -0.33897362 0.04852868 0.24684466 -0.016577714 0.23365434 0.07455878 0.16613184 -0.016965465 0.02436819 -0.227625669 -0.0004191321 -0.12194013 -0.111578239 -0.041314905 -0.09052165 -0.097587342 0.17721669 0.085952083 -0.28194043 -0.05932238 -0.057205746 5.321372e-02 -0.36367249 -0.015363998 0.142925944
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP -0.0934159787 0.060976175 -0.26757898 0.202795542 0.127852418 0.116405632 -0.105679519 -0.207537683 -0.127761790 -0.21806297 -8.009341e-02 -0.0570496808 0.35572293 -0.16622240 -0.23033722 -0.003656037 -0.24351471 -0.08281439 -0.21385192 0.089045910 0.05702248 0.162830271 0.1073197522 0.18581478 -0.043297663 0.140169126 0.16915870 0.130244227 -0.19356051 -0.078973917 0.21181563 0.09276215 0.124145090 -2.047438e-01 0.27452947 0.097684909 -0.088142625
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP -0.2531769445 -0.076391547 -0.35524046 0.178419647 -0.027932256 -0.062111318 -0.190294011 -0.401869438 -0.047034396 -0.09050315 -7.353341e-02 -0.0001531211 0.17442433 -0.05326287 -0.19853240 -0.023615069 -0.28054125 -0.06056164 -0.13689646 -0.006535930 -0.05171414 0.065779649 0.0174894144 0.18666747 0.145560303 0.080587372 0.12046867 0.174873906 -0.04655476 0.182351256 0.20782555 0.13377643 0.169157456 1.914065e-01 0.28928058 0.137016903 -0.018630858
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP -0.1411454025 0.047900582 -0.25625196 0.269176774 0.181462253 0.034784740 -0.116174263 -0.301870796 -0.044968652 -0.14811820 -8.208908e-02 -0.0352154619 0.29059194 -0.07287436 -0.20680686 0.017363938 -0.30032548 -0.11323896 -0.17005992 0.006601310 -0.06746557 0.077409057 0.0159590455 0.26558390 -0.037694782 0.167440913 0.21207543 0.140875368 -0.19160167 -0.060321378 0.24086742 0.10370036 0.094599476 2.850367e-02 0.28597165 0.029669499 -0.164314548
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP 0.1116529885 0.292188184 0.34831334 -0.123581722 0.050516147 0.145019714 0.206187041 0.163406743 0.007821523 -0.09940156 4.141215e-02 -0.0228886983 -0.05491470 -0.03095383 0.10860314 0.072183090 0.13099797 0.06711451 -0.07673696 0.041966891 0.25476428 0.177618166 -0.0154400900 -0.13870532 -0.100030138 -0.108760557 -0.10667785 -0.165118186 -0.21136962 -0.308830865 0.01307193 -0.01994302 -0.006007855 -5.126714e-01 0.03798671 -0.170143211 0.001351049
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP 0.2745402112 -0.044177556 0.31876654 -0.329339068 -0.105691495 -0.142140913 -0.003162191 0.157173800 0.089932849 0.07302904 -1.286126e-02 0.0758662612 -0.43830863 0.10777430 0.12826241 0.012040783 0.27425517 0.11749725 0.05930217 0.038952950 0.07519665 -0.100333208 0.0973981350 -0.10538721 -0.085077261 -0.021507687 -0.12994877 -0.094083007 0.20864101 -0.006430176 -0.19660903 -0.01719751 0.009752194 -1.663727e-01 -0.31852933 -0.004341272 0.203116535
FRASOR_TAMOXIFEN_RESPONSE_UP 0.2257957178 0.048434395 0.37131451 -0.247543764 -0.045657194 0.045635878 0.177470440 0.343445989 0.118508293 0.14408488 1.239577e-01 0.0438059242 -0.29647471 0.08855053 0.19195553 -0.026278996 0.24448407 0.11560848 0.07867322 -0.017378686 0.01098018 -0.168135671 -0.0825024498 -0.12893972 -0.172576527 -0.076678534 -0.18549006 -0.155205808 0.02425944 -0.011353726 -0.15818606 -0.07181830 -0.088612281 -2.797678e-02 -0.36273060 -0.104253429 0.030828162
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP -0.2233367530 -0.007741796 -0.37463807 0.260361044 0.062097031 0.042551473 -0.111730786 -0.361252426 -0.028706282 -0.04328331 -4.884767e-02 0.0149329143 0.25979025 -0.12316554 -0.20828246 -0.016039857 -0.15973390 -0.13573929 -0.06858283 0.107131118 -0.19184527 0.008118677 -0.0431836820 0.18748450 0.078381562 0.029201247 0.23179224 0.070307687 -0.20823179 0.030900475 0.23092058 0.16884357 0.117332432 1.166270e-01 0.32408086 0.047668182 -0.034181119
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP 0.1108356219 0.072625095 0.35562137 -0.266060947 -0.107490386 -0.048812016 0.183603465 0.203732983 0.195010034 0.30190337 5.026785e-02 0.1833451993 -0.21665967 0.10730554 0.19889431 -0.080954542 0.22126893 0.13154304 0.03614184 -0.220001339 0.11292678 -0.131457134 -0.0455743876 -0.27755754 -0.067880624 -0.016925423 -0.14254500 -0.174080097 0.03526815 -0.091897678 -0.03194165 0.07521659 -0.066452401 -4.426222e-02 -0.30126507 -0.155867534 -0.087824518
WATANABE_COLON_CANCER_MSI_VS_MSS_UP 0.1604393078 -0.046725031 0.24421714 -0.212744255 -0.088335734 -0.062050470 0.127640749 0.301282112 0.079637731 0.15503451 6.223935e-02 0.0203861980 -0.31159126 0.10664368 0.22892309 0.049192090 0.18292270 0.10162373 0.19409459 -0.004813772 -0.08510377 -0.099590371 -0.1592289695 -0.14987100 0.008425516 -0.293152578 -0.28643062 -0.040028563 0.18403042 0.088763148 -0.17183112 -0.07892018 -0.072561676 -5.959037e-03 -0.33781668 0.018589804 0.192669206
>
GSVA.Rcheck/tests/test_ssgsea_newapi.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> ## 2023-11-10 axel: simple test script for method ssGSEA, new API
>
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db
> library(GSVA)
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 1.4171739 -1.3444519 -0.99052898 0.4203395 1.30716224
g2 -0.7281951 0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754 0.09779699 -0.6792548 -0.09124045
g4 1.0735382 1.3156255 0.15588330 -1.8079608 0.48531108
g5 0.7229884 -0.9162342 1.93982245 0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> ssgseaPar <- ssgseaParam(X, gs)
> ssgsea.es <- gsva(ssgseaPar, verbose=FALSE)
> dim(ssgsea.es)
[1] 100 30
> ssgsea.es[seq.int(min(nRowsToPrint, nrow(ssgsea.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 0.050046308 0.153445680 0.06440230 0.245928762 -0.039281351 -0.009166497 0.15513670 0.05825828 0.075703720 0.2211977472 0.1909755963 0.213798011 -0.061198758 0.067211285 0.14116126 0.172193009 -0.076107078 0.146208482 0.27199640 0.027375283 0.25958081 -0.106935451 0.01955332 0.31199267 0.18689996 -0.02538041 0.025160949 0.10202723 0.317960731 -0.077195317
gs2 0.081171485 0.161930448 0.19635614 0.226977722 0.084705475 0.122712065 0.25375216 0.06124718 0.245645786 0.0213152908 0.1553307677 0.123198146 0.188559702 0.090605381 0.13634300 0.045583205 0.117061823 0.170602582 0.25518183 0.162276466 0.09782367 0.004672292 0.14429067 0.23905295 0.15842119 0.17958482 0.278174676 0.12969068 0.012534148 0.036195649
gs3 0.155539308 0.008842632 0.17903935 0.114060106 0.107208758 0.184963019 0.11327060 0.17081118 -0.110611530 0.3187327429 0.0896885519 0.169232189 0.292515661 -0.109522283 0.39211201 0.036070929 0.141878189 0.192157970 -0.01831034 -0.028374783 -0.31739185 0.238016028 -0.06330888 0.16972085 0.38536400 0.19915210 0.020583043 0.25012966 0.186034734 0.232849532
gs4 0.100407452 0.178458402 0.10660518 0.159340098 0.150690547 0.242066049 0.09044728 0.13980211 0.072737831 0.1082857648 0.0915659224 0.136234969 0.061324248 0.115973559 0.28107234 0.138134111 0.214028524 0.086667572 0.09385724 -0.029785545 0.12586634 0.082632971 0.17808866 0.21133946 0.16632346 0.17155219 0.102324377 0.20705832 0.099089588 0.290472119
gs5 0.194033575 0.062793781 0.04848598 0.217341759 0.191914352 0.129512577 0.15090606 0.27146643 0.219627621 0.1165628347 0.1379487730 0.152302042 0.099901051 0.205679023 0.12986947 -0.004963142 0.190709801 0.174401755 0.04427775 0.082055507 0.10896263 0.068825475 0.07614058 0.13558182 0.10568477 0.11492927 0.188047631 0.14065184 0.172431746 0.144376505
gs6 0.025988630 0.233512601 0.04485374 0.149671413 0.164451696 0.223396448 0.13735451 0.15303178 0.125071887 0.2456561342 0.1220311380 0.059904884 0.034633361 0.006225782 0.14294390 0.105914640 0.118989560 0.234603796 0.05542837 0.175273940 0.12454592 0.055488242 0.25878309 0.07422275 0.08197481 0.27581388 0.111785007 0.10024739 0.028180564 0.147366318
gs7 0.121579155 0.248146053 0.20935405 0.098421904 0.005775149 0.141790217 -0.04190763 0.02191384 0.225359966 0.0003605319 0.1938341367 0.218166804 0.234711429 0.171511561 0.14870761 0.004943158 0.168428297 0.131664402 0.16148235 0.046908832 0.09016756 0.199893820 0.17366414 0.10055547 0.08930753 0.16771471 0.141067369 0.20184683 0.113755713 0.062537548
gs8 0.175951236 0.104036859 0.16715411 0.066581368 0.124736570 0.107121162 0.15227018 0.13551209 0.066044097 0.0704654595 0.2006164228 0.164797947 0.149994634 0.063391557 0.20349135 0.205315802 0.006936426 0.130049520 0.17910706 0.061817683 0.05195776 0.059676074 0.18475605 0.10873217 0.25833265 -0.05691274 0.152978263 0.16063583 0.115089785 0.086840652
gs9 0.012967426 0.095461238 0.31825984 0.426422393 -0.206013607 -0.324946275 0.08738730 -0.14420537 0.061606991 0.1058375433 0.3407494698 0.060782012 0.036354426 0.158643593 0.02660000 0.070018029 0.295526014 0.370485869 0.31177819 -0.048490861 0.14293901 -0.052155641 0.39443397 0.18784912 -0.02491664 0.42956908 0.004366843 -0.09351215 0.539660825 0.194470958
gs10 0.310450557 -0.155381634 -0.04662343 0.069903089 0.235460838 0.136094565 0.35534293 0.14451145 0.032811542 0.2783927322 -0.0003708892 0.364801135 0.085153930 -0.007025257 0.31541487 0.214116068 0.076379415 0.300464786 0.02436326 0.014174550 0.29010030 0.353773500 -0.14036272 0.31414362 0.07517937 -0.36240056 0.135363804 -0.03291463 0.153638245 -0.006111044
gs11 0.148113831 0.288039198 -0.01173447 -0.125211500 0.422877496 0.368992470 0.31511056 0.11703945 0.119067901 0.2969431165 0.1767112563 0.269003140 -0.126699232 0.063371585 -0.15584600 -0.181509478 -0.252102260 0.084592131 0.41484382 0.102741674 0.19038088 0.155665264 0.11205065 0.18151841 0.07962262 -0.12707952 -0.043348625 0.52382483 0.471772841 0.192133037
gs12 0.191362265 0.075821020 0.10101534 0.015589766 0.118539915 0.150230064 0.11740963 0.09874133 0.196307720 0.1336100372 0.2243542624 -0.037860476 0.035827902 0.019570602 0.05739397 -0.086404343 0.090407547 0.090844017 0.11188849 0.250652019 0.15642076 0.100960304 0.13217523 0.09147595 0.14935140 0.07679723 0.164747489 0.10884565 0.021875796 0.224835781
gs13 0.291858703 0.346475308 0.21825672 0.130219327 -0.045991328 0.234867271 0.34027295 0.11127727 0.246617815 0.3200429439 0.0493766799 0.008390396 0.100929397 -0.036222987 0.09552925 0.116070504 0.050409473 0.117373720 0.33645267 0.196460577 0.28151964 0.250645402 0.00786962 0.16471272 0.26987750 0.14003078 0.274510723 -0.06972362 0.111250445 0.031727494
gs14 0.190335262 -0.064441167 -0.14720764 0.313073121 0.184851969 0.034311372 0.29316721 -0.12497882 0.099774835 0.0064937265 0.1376061089 0.105283947 0.322046351 0.260972829 0.22468693 0.113901307 0.002316888 0.174550489 0.03848764 0.149291379 0.16606614 0.171358521 -0.23264680 0.06333781 0.26046384 0.14647155 0.061583955 0.07893101 0.084042439 0.241795872
gs15 0.217913642 0.141978343 0.21703088 0.061088530 0.048906153 0.109096881 0.04362714 0.21225573 0.180978230 0.1203085545 0.0888328589 0.183656898 0.074251458 0.108846516 0.01790968 0.222984303 0.115016738 0.124120115 0.11555410 0.162960343 0.12134445 0.108547160 0.18775900 0.20267430 0.21813681 0.05956895 0.081086983 0.04401661 0.004584748 0.113053205
gs16 0.008372193 0.198823477 0.02924146 0.187858615 0.054689339 0.068398317 0.10730408 0.05120743 0.070935563 0.0784796201 0.0060339391 0.097386464 0.181367848 0.060028026 0.18405253 0.129145564 0.127244708 0.083034338 0.06835057 0.111075315 0.12519485 0.101386193 0.10027865 0.07630206 0.11786623 0.12151097 0.076099407 0.06340149 0.199302468 0.107472386
gs17 -0.021209113 0.041234441 0.15849782 0.140830687 0.094989136 0.050310553 0.27875609 0.19671686 0.224090634 0.0823059119 0.1446622842 0.073610528 0.181135843 0.128995630 0.18515033 0.043619934 0.156832276 0.139817243 0.12097998 0.094078972 -0.01250999 0.263313353 0.18157262 0.06476920 -0.02611791 0.19436554 0.098776218 0.15857389 0.086521226 0.140174046
gs18 0.224221766 0.208703330 0.19566999 0.277362679 0.086022967 0.155782407 0.21984017 0.06224476 0.184311430 0.0746810884 0.1500112520 0.031591001 0.218220154 0.085782290 0.05403013 0.239733411 0.225608272 0.080410483 0.12419147 0.087988742 0.09109210 0.118154979 0.18042347 0.15034333 0.05419059 0.06131728 0.135992696 0.05116987 0.008007108 0.258350779
gs19 0.060496086 0.192359984 0.06580294 0.039342129 0.056421351 -0.050071255 0.09835605 0.19838255 0.232365057 0.1878213634 0.0597175977 0.113955441 0.138654652 0.118112400 0.02948580 0.183873151 0.295382463 0.084940527 0.01555718 0.237711415 0.15405004 0.113893226 0.01261294 0.08150703 0.13679835 0.17664342 0.264724147 0.09871800 0.219093664 0.229287431
gs20 -0.002331868 0.104835345 0.19095558 0.196525176 0.230511428 0.196485997 0.20691704 0.06292261 0.195484717 0.0748935120 0.2274655731 0.234958644 0.100720547 0.098787011 0.01322616 0.215826190 0.107383744 0.272734953 0.14006653 0.128606660 0.17526232 0.154071267 0.20185690 0.16029505 0.11767405 0.04019989 0.087560954 0.12297014 0.120555888 0.165784444
gs21 0.235531812 0.174101071 0.04331386 0.066700909 0.161550174 0.127508845 0.22978825 0.07748909 0.142407170 0.1262273951 0.0698341132 0.023900707 0.157264078 0.064306708 0.19037040 0.022272735 0.085059711 -0.030333898 0.10370986 0.041024634 0.15543738 0.156630569 0.11755610 0.14827641 0.09418257 0.26082349 0.175064303 0.10818015 0.134571164 0.137789233
gs22 -0.047650929 0.186841315 0.03222656 0.119471610 0.193877261 -0.031790084 0.29277495 0.07689763 -0.019411157 0.0595495594 0.3807452330 0.071668171 0.135528037 0.177342300 0.18766862 0.143986114 0.138391599 0.137573467 0.11420368 0.222882426 0.06096151 0.160136193 0.37542340 0.34681913 0.02224170 0.20670334 0.053159207 0.38290841 0.093613064 0.168206100
gs23 0.144199311 0.186850465 0.09563174 0.191503633 0.197926948 0.183687676 0.08857992 0.08438396 -0.002354026 0.1015861893 0.1556606664 0.149031544 -0.003876439 0.220881227 0.19108193 0.128779302 0.115583034 0.128810013 0.21233978 -0.001768056 0.13275623 0.154387029 -0.06742232 0.07991395 0.15197278 0.23716849 0.161038324 0.06541124 0.045781546 0.096529440
gs24 0.244519906 0.255495479 -0.02212643 0.007561398 0.045577309 -0.009892961 -0.04971968 0.19698687 -0.078933887 0.0414502136 0.3742714753 -0.050544352 0.013590683 0.003608241 -0.34825490 0.415098155 0.138025957 -0.001864139 -0.37016901 0.117420895 0.37252626 -0.116751635 0.32072205 -0.06702968 0.11533867 0.21077948 -0.041474525 0.03217032 -0.044872621 0.165434542
gs25 0.193601681 0.091245208 0.18463093 0.100724310 0.055381436 0.002669872 0.08514397 0.05620041 0.124029775 0.1800670374 0.1742834586 0.170840558 -0.034319609 0.177918537 0.09381717 0.145284931 0.208953543 0.324830001 0.16350519 0.037554150 0.26681356 0.012083285 0.28774452 0.13816374 0.05451236 0.10453580 0.280375699 0.12512785 0.135834785 -0.038267879
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+ grep("^REACTOME", names(c2BroadSets)),
+ grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- ssgseaParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+ minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.21698978 0.190101718 0.20525435 0.21623854 0.228779757 0.20936853 0.22506971 0.2234235687 0.220780261 0.21444921 0.21903592 0.220664804 0.20924941 0.21012248 0.20502111 0.19985724 0.19721755 0.1913957094 0.225134348 0.21709921 0.20425590 0.201712948 0.19379346 0.23122161 0.221525326 0.212463371 0.22792181 0.221128254 0.204351144 0.218947974 0.222579602 0.229420498 0.22060750 0.20299621 0.21904369 0.215493102
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.32433043 0.330666662 0.31869186 0.30766734 0.322670342 0.31519248 0.31986814 0.3185006606 0.329706974 0.31265435 0.32676917 0.331734849 0.31520463 0.32288700 0.31043279 0.31220717 0.30722070 0.3168181879 0.320522995 0.32920820 0.31023554 0.313528956 0.32324416 0.32442285 0.307746225 0.302000352 0.31422539 0.325061712 0.324433443 0.320805701 0.313120479 0.322340322 0.32303440 0.31470507 0.32982874 0.322774682
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.32613456 0.292246085 0.32171779 0.31922331 0.327342371 0.32285413 0.31703691 0.3267972444 0.317799481 0.30548746 0.32071494 0.325200548 0.31574521 0.32222525 0.30445849 0.31198274 0.30056356 0.3175363433 0.313248908 0.31537383 0.31498239 0.312138133 0.31157241 0.31348063 0.313260085 0.305543436 0.31306655 0.318602720 0.309415331 0.316959102 0.307805386 0.319474001 0.30318847 0.31470071 0.31941053 0.326759498
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.14142675 0.152207936 0.14238572 0.07942752 0.105050011 0.12961280 0.11296245 0.1601888948 0.141345242 0.09869492 0.16412075 0.158434716 0.10823031 0.17672793 0.13428568 0.11392145 0.14170168 0.1428868433 0.146955737 0.14818936 0.17164951 0.138839694 0.12229281 0.11673825 0.109550600 0.069456602 0.14040696 0.182050959 0.114699787 0.189319064 0.130300608 0.111638487 0.14391952 0.12318954 0.12224946 0.137976483
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.15550203 0.118146628 0.14707933 0.18705703 0.199943713 0.16410186 0.16813615 0.1802125060 0.170259262 0.18671240 0.18252531 0.164279928 0.16794179 0.17149276 0.16625970 0.14528892 0.13398404 0.1378452121 0.169092878 0.19220147 0.19047757 0.157694632 0.12722729 0.18630354 0.195343439 0.176599720 0.19802720 0.161573744 0.152184181 0.173797461 0.187295272 0.197591583 0.17232864 0.16136207 0.17911558 0.180031024
KEGG_GALACTOSE_METABOLISM 0.11149473 0.103217880 0.11085844 0.13741766 0.165952026 0.14418332 0.12726683 0.1370210459 0.142805283 0.15242781 0.15221252 0.149682255 0.15018345 0.14626213 0.11999955 0.11557928 0.11593006 0.1148701557 0.149672283 0.16891575 0.16494312 0.123919369 0.09211866 0.14937665 0.176575543 0.129061875 0.17075453 0.137859374 0.112830567 0.139888692 0.144650768 0.159081145 0.13428014 0.12448791 0.15631215 0.169827420
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.04198555 -0.032292278 0.01406413 -0.01064716 -0.022308338 -0.03194340 -0.01037135 0.0661161558 -0.007360627 -0.02923521 0.01141517 0.001497673 -0.01420985 0.03438381 -0.03203514 -0.01804054 -0.01538922 -0.0026678425 0.027398691 -0.04882214 -0.11561188 -0.008509357 -0.01203473 -0.02089645 0.001083068 -0.003061739 -0.11355468 0.027193644 -0.020507654 0.050375480 0.023851383 0.004333629 0.02757450 -0.01461678 -0.01931510 0.006947649
KEGG_FATTY_ACID_METABOLISM 0.19144010 0.177618186 0.19229237 0.18162156 0.195013260 0.17285053 0.18737923 0.2094263692 0.189298006 0.17744684 0.17726086 0.187594417 0.17484769 0.18064373 0.17580318 0.16279037 0.17715535 0.1847771315 0.187298535 0.17615351 0.15131681 0.184344838 0.17544154 0.18540490 0.164558082 0.179209973 0.15666232 0.189591897 0.183358359 0.189661362 0.185937924 0.195641028 0.20399213 0.18301653 0.17977089 0.185912168
KEGG_STEROID_BIOSYNTHESIS 0.29508326 0.295486909 0.26286536 0.27906495 0.291220515 0.28574075 0.30491564 0.3028446031 0.306065643 0.26781522 0.29464863 0.281727962 0.28372727 0.30309918 0.30917324 0.26593252 0.26945212 0.3018824439 0.272449306 0.28920242 0.27852421 0.273019343 0.28299044 0.28594314 0.297497744 0.264419747 0.26785147 0.276188961 0.286487520 0.308034927 0.289095316 0.299848680 0.29269188 0.29943769 0.29468427 0.287313424
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS -0.03581753 -0.092130799 -0.04761225 0.05891582 -0.123502963 -0.08482548 -0.02276997 -0.0448787260 -0.064166255 -0.15073085 -0.07715570 -0.027840150 -0.03137614 -0.08997226 -0.12858747 -0.15452411 -0.15192399 -0.0008490506 -0.141927194 -0.12439918 -0.14957231 -0.052218742 -0.06096819 -0.03648457 -0.146524551 -0.129025468 -0.15339387 0.017340701 0.013213935 0.021006051 -0.008592746 -0.079442545 -0.01531376 -0.09542512 -0.12181560 -0.100962579
KEGG_STEROID_HORMONE_BIOSYNTHESIS -0.00603142 -0.048459074 -0.07974466 -0.01648330 -0.091376743 -0.04645294 -0.05783215 -0.0077100648 -0.032440674 -0.04925962 0.01257962 -0.027085733 -0.05133063 -0.03464357 -0.09107591 -0.04604528 -0.06313163 -0.0037229305 -0.083744196 -0.04403506 -0.07403528 -0.041751578 -0.06718897 -0.06224135 -0.022813686 -0.063619976 -0.05046193 -0.046775240 -0.007732293 -0.031014587 0.038972593 -0.058183774 0.01398730 -0.04158946 -0.10044713 -0.022828144
KEGG_OXIDATIVE_PHOSPHORYLATION 0.23470278 0.265724094 0.26337583 0.24721506 0.255184437 0.25137871 0.25453660 0.2566994039 0.246493165 0.25745496 0.25786805 0.247495875 0.25321032 0.26043249 0.24844391 0.24615206 0.25180784 0.2621473829 0.253121007 0.24466091 0.24444401 0.248324354 0.24596943 0.26085564 0.252493166 0.259461341 0.25704694 0.244689333 0.244937049 0.247126050 0.249275632 0.253150955 0.25606696 0.26126201 0.26134069 0.248688913
KEGG_PURINE_METABOLISM 0.11282696 0.113448858 0.13052367 0.12872555 0.130498773 0.12514834 0.12708974 0.1254518508 0.114374092 0.11746139 0.12720504 0.123909976 0.12501986 0.12926543 0.11864833 0.11039303 0.11837407 0.1306561048 0.120874877 0.11874917 0.12461513 0.118754355 0.11004336 0.12341313 0.111728921 0.125220817 0.12599093 0.120422095 0.116669899 0.120942649 0.125716426 0.120651681 0.12066825 0.12286847 0.11781015 0.119089666
KEGG_PYRIMIDINE_METABOLISM 0.17757771 0.175394817 0.19858724 0.19679890 0.184451412 0.18857531 0.19443581 0.1913521689 0.176616057 0.18757690 0.18742386 0.190866974 0.17707165 0.19343157 0.18609589 0.18058113 0.18517942 0.1962563816 0.174386960 0.18912297 0.18783617 0.175188077 0.17750981 0.19040712 0.177216013 0.198853296 0.18467609 0.173153515 0.179616517 0.173598395 0.177726615 0.185542608 0.19263573 0.19211082 0.17683259 0.184513099
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.10989042 0.093058240 0.09075182 0.09975330 0.110553924 0.08932985 0.10833717 0.1022932484 0.098714538 0.09452201 0.10412503 0.112821342 0.09845573 0.09864529 0.10839464 0.10195788 0.09460140 0.0890330658 0.114926416 0.12373452 0.09891343 0.096051085 0.08806549 0.11101748 0.101678482 0.090367626 0.10014984 0.113927079 0.088757290 0.111944663 0.101911619 0.091610295 0.08631087 0.10449490 0.09680798 0.113666733
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.07589995 0.013164475 0.03073650 0.05497730 0.075187517 0.04629436 0.05684194 0.0721291176 0.091914474 0.05519977 0.08746496 0.050067541 0.05965801 0.06067566 0.08409397 0.10238484 0.01501362 0.0045650662 0.049144983 0.07054669 0.05116744 0.045186268 0.05137738 0.06424885 0.085465393 0.053004029 0.06129235 0.050492310 0.064513199 0.069147728 0.067789023 0.075006091 0.03311465 0.05179666 0.09353812 0.069833588
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.25896290 0.229197097 0.23915083 0.24454874 0.251021905 0.23616587 0.24671301 0.2542987322 0.256828445 0.24146968 0.26145521 0.245522688 0.24379502 0.24900959 0.26862910 0.25530625 0.22947514 0.2349385424 0.237967026 0.24111547 0.26557949 0.234639477 0.23412745 0.23301781 0.258395796 0.215746987 0.23465476 0.256687996 0.239987950 0.250370070 0.237026241 0.252743721 0.22651684 0.23865720 0.25741554 0.244270299
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.18843747 0.186649426 0.17530857 0.15633381 0.178282757 0.18033157 0.18581500 0.1963894497 0.191659866 0.14190172 0.20151595 0.181514394 0.18800238 0.18208434 0.18884446 0.17012565 0.16953990 0.1676338847 0.183699227 0.19745711 0.16337494 0.161194552 0.15788716 0.18351104 0.171161284 0.163754665 0.15047991 0.196948812 0.185610694 0.198192986 0.174172878 0.182779264 0.17802037 0.16062757 0.19890618 0.189941640
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.28568183 0.282786776 0.24961716 0.24491634 0.270528716 0.29605800 0.25836996 0.2521218808 0.281679472 0.24721670 0.32053768 0.274690843 0.28302481 0.30038542 0.30322093 0.29120270 0.28253548 0.2579537498 0.267208046 0.32453395 0.29189041 0.267396603 0.24747811 0.28281020 0.293967599 0.262178623 0.29429367 0.269346291 0.263428379 0.266865452 0.261098171 0.251262879 0.25119395 0.28412517 0.31296991 0.299112229
KEGG_LYSINE_DEGRADATION 0.11363066 0.093971946 0.11756645 0.11921555 0.114150109 0.11417055 0.11382771 0.1282543770 0.110373515 0.10264637 0.10896281 0.119922709 0.11111424 0.09923486 0.10398550 0.09158226 0.11014421 0.0992105519 0.114396655 0.11105307 0.10519398 0.095412052 0.09666140 0.10310679 0.108674463 0.114399506 0.09091906 0.108210445 0.111356587 0.117142092 0.103818204 0.110313192 0.10414576 0.09228489 0.10733176 0.111914878
KEGG_ARGININE_AND_PROLINE_METABOLISM 0.12738384 0.120646580 0.12800721 0.12780121 0.140190182 0.11234716 0.13886310 0.1363147983 0.118339180 0.12495239 0.13387648 0.119717717 0.12674429 0.11413969 0.12760775 0.12051016 0.11112441 0.1060723468 0.135207120 0.11384185 0.11270554 0.120444480 0.10890719 0.13671193 0.148306216 0.127590175 0.12033740 0.129990177 0.120085884 0.143513369 0.139267799 0.139711646 0.12631236 0.12302536 0.13671696 0.129915338
KEGG_HISTIDINE_METABOLISM 0.01037506 -0.009232361 -0.02503732 -0.04007054 -0.004116879 -0.02891744 -0.02515002 0.0005514458 -0.015393247 -0.03216059 -0.03701174 -0.018066447 -0.04417577 -0.03579879 -0.02417860 -0.02971581 -0.02648223 -0.0314952886 0.009196744 -0.04701498 -0.06879069 -0.022838496 -0.03099772 -0.03704899 -0.025519728 -0.039940345 -0.08649494 0.003895911 -0.029842438 -0.000484478 -0.020239498 -0.027308388 -0.01132841 -0.03055363 -0.02153193 -0.036015417
KEGG_TYROSINE_METABOLISM 0.06714488 0.053002829 0.05753161 0.04337986 0.057065867 0.05794194 0.05847814 0.0507298323 0.058615853 0.04701795 0.05759954 0.046542561 0.04954693 0.06556692 0.07181820 0.05370509 0.05763770 0.0690302934 0.044285470 0.04352433 0.06313789 0.067191326 0.04882973 0.05342728 0.052557681 0.041207045 0.04378767 0.064256091 0.055186897 0.048349590 0.069931678 0.042623088 0.06573735 0.06531103 0.05853359 0.057231880
KEGG_PHENYLALANINE_METABOLISM 0.11960304 0.096377593 0.09464200 0.09061793 0.091267769 0.09170094 0.09990226 0.0976280231 0.105007097 0.08739764 0.09597757 0.092011591 0.10469452 0.09925149 0.10437604 0.10710066 0.07942615 0.0989797292 0.119065427 0.09925727 0.10453704 0.086330586 0.09687302 0.10521245 0.097635425 0.085996013 0.09971671 0.107245185 0.084152959 0.091621331 0.102207053 0.107399793 0.10262963 0.09509872 0.08816275 0.098383108
KEGG_TRYPTOPHAN_METABOLISM 0.12707074 0.135904404 0.12002196 0.10198472 0.105456181 0.10258554 0.11263398 0.1471089408 0.134184467 0.09404104 0.12387419 0.114507791 0.10212085 0.12955711 0.09526545 0.11899775 0.10760770 0.1237862285 0.125934177 0.11873044 0.06658891 0.112588368 0.11212948 0.10011186 0.118024833 0.113614802 0.09153418 0.132524487 0.110393708 0.120368868 0.125229509 0.116181945 0.14682099 0.11978502 0.10429972 0.118580441
> pickrellPar <- ssgseaParam(pickrellCountsArgonneCQNcommon_eset,
+ canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esrnaseq[seq.int(min(nRowsToPrint, nrow(esrnaseq))),])
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.256075759 0.234440285 0.22365541 0.25164814 0.25617134 0.22440002 0.26825331 0.24363221 0.22303626 0.24453749 0.241659658 0.24784931 0.240912314 0.26440850 0.25175671 0.221994177 0.25951673 0.257749187 0.23737636 0.23373922 0.24102923 0.24394811 0.24421325 0.253552534 0.230189600 0.233117341 0.25308269 0.25087262 2.352772e-01 0.25308477 0.25405537 0.23991583 0.23478740 0.24563546 0.25646515 0.25071702
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.276806659 0.263840724 0.24698443 0.27529933 0.27555689 0.24975236 0.28827170 0.26740093 0.22453250 0.25824366 0.264578233 0.26626941 0.267999750 0.27293682 0.26955574 0.218915231 0.28141656 0.274122454 0.25380024 0.25929889 0.26072040 0.26865139 0.27076349 0.265378539 0.244259988 0.241425821 0.28531051 0.28111746 2.409079e-01 0.26208495 0.26235839 0.27393384 0.25428617 0.26899433 0.27380231 0.26464529
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.308157944 0.298087515 0.29014344 0.31316947 0.31075726 0.29580575 0.33150923 0.30911766 0.27215128 0.29310006 0.318390367 0.31750877 0.303315781 0.32990830 0.31603865 0.276156993 0.32137928 0.328904420 0.28873356 0.28984710 0.29765756 0.29417757 0.30408635 0.309010795 0.284366223 0.286933996 0.32289659 0.31674788 2.939716e-01 0.30287805 0.30290168 0.30124596 0.29981504 0.30880460 0.29585316 0.31112043
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.072900627 0.058114116 0.05095095 0.05552091 0.06878391 0.07768438 0.08213775 0.09250688 0.03556826 0.09156620 0.097878249 0.06956272 0.081520495 0.14591883 0.10114649 0.031874974 0.09204189 0.115726730 0.08879480 0.08133511 0.11303741 0.04597980 0.05930134 0.091652196 0.045442518 0.015179733 0.11243384 0.13618849 5.819542e-02 0.07901269 0.10767281 0.06217197 0.10083457 0.07884946 0.04823275 0.08069438
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.179143833 0.181466412 0.18164218 0.20648051 0.16508263 0.15692126 0.20526979 0.18220460 0.12828973 0.18948921 0.194624757 0.18678502 0.191651374 0.18621396 0.21686165 0.163982758 0.20153270 0.213681011 0.17124101 0.18326784 0.17747109 0.18055651 0.18666452 0.208603904 0.182698854 0.186529878 0.20249678 0.14324407 1.692164e-01 0.17589451 0.20061610 0.16286430 0.16195031 0.19908025 0.18482874 0.20501174
KEGG_GALACTOSE_METABOLISM 0.181131627 0.159926813 0.16270579 0.20573093 0.18044266 0.15543518 0.21952142 0.17843456 0.12359001 0.18349838 0.199111340 0.19452033 0.190574177 0.19551040 0.22253670 0.149654098 0.20567552 0.200581366 0.17030505 0.18223148 0.18954484 0.17613758 0.17006314 0.194920826 0.198422033 0.192448054 0.22245521 0.15408689 1.635711e-01 0.17252060 0.20589447 0.15895753 0.15412635 0.18901486 0.18924635 0.20842567
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.076244940 0.080303827 0.01896975 0.05351930 0.05634166 0.03667802 0.08143338 0.05261833 0.02095408 0.09594147 0.046490176 0.03601321 0.072687156 0.13959149 0.04107588 0.001557203 0.08580840 0.109000508 0.05530623 0.01833645 -0.08023056 0.01932496 0.06300957 0.066003820 0.023771292 0.007102489 0.03086936 0.10270298 -3.157042e-03 0.05314639 0.07495172 0.08280269 0.05626948 0.04257381 0.06298584 0.07433531
KEGG_FATTY_ACID_METABOLISM 0.189817509 0.170872559 0.14155879 0.19190458 0.20061758 0.16220943 0.20719303 0.18088378 0.16687336 0.17684223 0.169286125 0.17914218 0.178915532 0.20998722 0.17201976 0.131109962 0.20936840 0.197325741 0.16514248 0.15827116 0.16387239 0.17860585 0.18319739 0.188238171 0.113651303 0.130750066 0.17770022 0.19465482 1.597647e-01 0.18876629 0.18911247 0.18967056 0.15979790 0.16688397 0.17911784 0.19754478
KEGG_STEROID_BIOSYNTHESIS 0.224283008 0.183502868 0.10641865 0.15431521 0.20673953 0.19381572 0.19919988 0.19375955 0.13759180 0.13279097 0.166353748 0.15479731 0.201859944 0.18441257 0.20240525 0.138935955 0.16161930 0.187730965 0.12780607 0.17277089 0.17211107 0.17687687 0.20523660 0.178291553 0.222139792 0.187421826 0.17910855 0.15862534 1.563029e-01 0.17970860 0.21186843 0.18641454 0.20553433 0.21995063 0.24238713 0.17376305
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 0.007298097 -0.045231480 -0.05615631 0.07155428 -0.03778360 -0.06475813 -0.01631200 -0.01120530 -0.07059793 -0.07173726 -0.040573532 -0.01433368 0.005000649 0.05037597 -0.04733764 -0.070668142 -0.04251391 -0.016724966 -0.03493901 -0.06316513 -0.04576571 -0.03089320 -0.02209954 -0.003440324 -0.082490284 -0.065017438 -0.04750185 -0.03693552 -2.405233e-05 0.03741013 0.04625340 -0.02630856 -0.04838299 -0.05724028 -0.04066866 -0.03635462
KEGG_STEROID_HORMONE_BIOSYNTHESIS -0.046018108 -0.093294319 -0.13746745 -0.05837140 -0.11437771 -0.04362896 -0.07770349 -0.07282807 -0.09993655 -0.05986338 -0.051748220 -0.07057083 -0.081288974 -0.04819890 -0.08749854 -0.080358972 -0.09355664 -0.072350610 -0.13131875 -0.06410751 -0.13561358 -0.09017416 -0.11589119 -0.085631744 -0.094304978 -0.119555451 -0.07166260 -0.03448379 -6.616326e-02 -0.10521967 0.02700273 -0.04856765 -0.05304776 -0.11560595 -0.12890981 -0.06549103
KEGG_OXIDATIVE_PHOSPHORYLATION 0.290044085 0.306375054 0.26041452 0.29564165 0.29454677 0.28682961 0.31516942 0.29225539 0.29624881 0.28190329 0.288965873 0.29838803 0.296122751 0.30714929 0.29408922 0.298005863 0.29592505 0.304180875 0.28081795 0.28727692 0.29838136 0.30109527 0.29148313 0.294331078 0.252378384 0.264546548 0.29654867 0.30641064 3.067693e-01 0.28941630 0.30210492 0.30197862 0.31189519 0.28625608 0.28901836 0.28725201
KEGG_PURINE_METABOLISM 0.121552424 0.114160233 0.11048165 0.13105255 0.11833540 0.10870679 0.12953106 0.12047921 0.08446782 0.11231713 0.112887563 0.11536146 0.105467789 0.13155054 0.12002126 0.113011238 0.12896358 0.123095976 0.11982023 0.10583172 0.10912082 0.11113234 0.10512995 0.109356079 0.099193918 0.103015548 0.12720303 0.13748276 1.143107e-01 0.12051435 0.10972889 0.11378580 0.10276405 0.11768950 0.10730690 0.11186763
KEGG_PYRIMIDINE_METABOLISM 0.159729043 0.145500125 0.14730788 0.17410916 0.15340765 0.14791645 0.16855838 0.15892991 0.11381615 0.15157687 0.147076658 0.15194721 0.127133366 0.17182833 0.15867282 0.142850963 0.16307797 0.161493787 0.14783129 0.14154301 0.14666943 0.14191003 0.14540419 0.146472588 0.114588161 0.131180250 0.16581516 0.18090777 1.515887e-01 0.16056284 0.13622778 0.16268189 0.13979801 0.15559869 0.13630535 0.15387683
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.112712342 0.074567957 0.08695191 0.09240285 0.11298142 0.09506027 0.09739823 0.07764648 0.10950728 0.07593407 0.076879433 0.07931452 0.081605261 0.10786533 0.09769440 0.046974792 0.08948356 0.076841077 0.09165978 0.07828511 0.07203344 0.08737763 0.06590033 0.087495399 0.073193496 0.070563832 0.10778181 0.09237847 6.349400e-02 0.12215027 0.08568016 0.06775927 0.05945302 0.08035606 0.08620309 0.09688249
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.063414089 0.008780948 0.05935336 0.06694159 0.06788012 0.04426421 0.03357666 0.04745672 0.07210759 0.05011682 0.019676287 0.05273708 0.007465601 0.07973086 0.04674425 0.006592034 0.03645575 0.007696429 0.06004590 0.01417259 -0.02089575 0.04782863 0.03721318 0.033513757 0.059026917 0.026399449 0.05354070 -0.01859829 3.487693e-02 0.09841955 0.03620653 0.02255710 -0.01427914 0.03857687 0.09608318 0.07059776
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.234037901 0.189794344 0.20539118 0.22853483 0.22730123 0.19920525 0.19855436 0.22105176 0.21859510 0.21569681 0.192366034 0.19664087 0.202877108 0.24438081 0.22600833 0.162641803 0.19791966 0.190679930 0.19704281 0.18167020 0.20854176 0.21380744 0.20125670 0.201679421 0.212128486 0.203347274 0.19742841 0.19425738 1.833991e-01 0.22861206 0.18710448 0.20444733 0.17838357 0.19817716 0.21897475 0.22036231
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.149779799 0.130868968 0.11141194 0.15213162 0.15707673 0.12253970 0.17713191 0.13281221 0.14628124 0.12815576 0.154689122 0.13889347 0.148455429 0.18582753 0.14490882 0.100438410 0.16119649 0.158609790 0.12845278 0.13377880 0.12834048 0.13474814 0.13427088 0.163849429 0.097733032 0.107920307 0.15085656 0.15995811 1.171796e-01 0.15812798 0.14524879 0.14585176 0.13929386 0.12933917 0.15265580 0.15760441
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.295088488 0.261790244 0.20437749 0.28756505 0.29611186 0.27215510 0.27635622 0.24614956 0.27920993 0.21961975 0.291130821 0.26258549 0.257402155 0.29814324 0.28934456 0.233740001 0.27822280 0.256193143 0.24326695 0.27454545 0.27722539 0.24789039 0.23212598 0.282819863 0.269379426 0.251031182 0.30807137 0.28499798 2.550574e-01 0.27349722 0.26662427 0.24049639 0.27670544 0.24397409 0.28271525 0.28462182
KEGG_LYSINE_DEGRADATION 0.141718140 0.125418015 0.13297959 0.14283107 0.13473057 0.12203529 0.14719941 0.13385750 0.09491781 0.12236495 0.122241586 0.12711931 0.124884910 0.13829366 0.13755243 0.119698191 0.14226579 0.133886134 0.14436915 0.11175177 0.10560139 0.13083694 0.13813000 0.135265809 0.112781050 0.123216658 0.12973261 0.13564156 1.232322e-01 0.13580749 0.12462139 0.13626539 0.10525941 0.13533806 0.13567788 0.14158147
KEGG_ARGININE_AND_PROLINE_METABOLISM 0.135734485 0.123178563 0.10586472 0.12564409 0.14906498 0.11818042 0.14021365 0.12277557 0.09432899 0.11770248 0.140202156 0.10961800 0.124468602 0.13170402 0.12160081 0.090198152 0.12999175 0.127112384 0.11788380 0.11428458 0.11762968 0.13710845 0.11356352 0.130539368 0.104547379 0.117760260 0.12573673 0.11179118 1.059606e-01 0.14634309 0.13320560 0.10643279 0.10948257 0.12483287 0.14500055 0.12996698
KEGG_HISTIDINE_METABOLISM -0.030831971 -0.026347382 -0.05246956 -0.03817025 -0.03711451 -0.05239151 -0.02992710 -0.04339704 -0.04535416 -0.02246956 -0.068943683 -0.05028602 -0.063113563 -0.02707367 -0.05323869 -0.063275978 -0.03173868 -0.039525683 -0.02755053 -0.04591086 -0.06760272 -0.03666616 -0.02528646 -0.040320656 -0.044784334 -0.057674857 -0.06783511 -0.02118087 -4.757559e-02 -0.03079779 -0.03306480 -0.03762207 -0.04374289 -0.03096278 -0.01254511 -0.03899109
KEGG_TYROSINE_METABOLISM 0.017578905 0.013796202 0.01327581 0.04762972 0.01224515 0.03037335 0.04467113 0.03453989 0.01369270 0.03704134 0.022735388 0.02729295 0.010396257 0.04953794 0.03065282 0.024393238 0.04694918 0.040233938 0.01044212 0.02743798 0.03891701 0.04757522 0.02613133 0.039036101 -0.011637129 0.007204219 0.04176325 0.02171444 5.394063e-02 0.02825620 0.04740187 0.02656193 0.05525311 0.01901562 0.06130051 0.03639278
KEGG_PHENYLALANINE_METABOLISM 0.039387037 0.029253986 0.02751646 0.04138092 0.02542332 0.04090945 0.02613385 0.04694566 0.04409473 0.02669409 0.009505697 0.01810860 0.029763207 0.06543376 0.04989771 0.029176209 0.03209528 0.037862444 0.04544696 0.01254836 0.07318278 0.05544060 0.05343313 0.038427201 0.007101842 0.043387306 0.05281127 0.02894583 3.058806e-02 0.04347886 0.06369582 0.02896260 0.02467872 0.04490225 0.06313854 0.01977051
KEGG_TRYPTOPHAN_METABOLISM 0.123296794 0.123012202 0.07613129 0.11525403 0.10856497 0.10334620 0.12704283 0.12708541 0.09159597 0.10202432 0.117859010 0.11469963 0.107325317 0.13152508 0.10459837 0.095553577 0.11230030 0.119066458 0.11008815 0.09174693 0.07821333 0.11181722 0.12158703 0.101828953 0.089254784 0.080564906 0.11224215 0.15882861 9.554444e-02 0.11310320 0.12619907 0.13651820 0.12255016 0.10789454 0.12458913 0.11276116
>
> gbmPar <- ssgseaParam(gbm_eset, brainTxDbSets)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up -0.04270256 -0.1050256 0.12398917 -0.19785894 -0.0706204 -0.08331645 -0.04587976 -0.02691259 0.1493980 0.07636271 0.1292104 -0.02880156 -0.10622416 0.08485902 -0.02108542 -0.10255611 -0.04955077 -0.06055262 -0.1843912 -0.002264514 -0.000616764 -0.08413483 -0.1282847 0.10064219 0.16233229 -0.08391388 0.129510723 0.006051755 -0.0957773 0.05930173 0.07585551 0.122092770 -0.01523058 -0.17022164 -0.02753735 -0.09626334 -0.16239668 -0.1442122 -0.08378182 0.086702046 -0.06829592 -0.01859185 -0.10794134 -0.04824622 -0.02360036 -0.07829131 0.02113254 0.12831408 -0.05187672 0.021500630
astroglia_up -0.24889633 -0.3181389 -0.16250310 -0.34518377 -0.2328486 -0.19025164 -0.20798167 -0.18978759 0.1634546 -0.18567656 -0.1220784 -0.14188750 -0.08219957 -0.18716765 0.08621605 -0.05093007 -0.23268801 -0.28527541 -0.2431186 0.280782610 0.051930564 -0.28603563 -0.2787882 -0.23358730 0.02706818 -0.17339069 0.007161405 -0.128829863 -0.2530055 -0.17991022 0.04954921 0.086976084 -0.19119326 -0.02761475 -0.10601965 -0.21094338 -0.17424458 -0.1764272 -0.25829321 0.183158653 -0.15279730 -0.15292932 -0.25484151 0.12260719 -0.09708606 -0.02624126 -0.03188327 -0.01503725 -0.17238517 -0.105109149
neuronal_up 0.41365516 0.1370905 0.02258175 0.04140498 0.3739370 0.02504198 -0.09469289 0.21037816 0.2898127 0.02594733 0.4223345 -0.22630258 -0.21649319 -0.12661321 0.05458802 -0.15745561 0.22021627 -0.22540274 -0.1018101 0.108388420 0.248267146 0.15400529 0.2284369 -0.03153927 -0.06967695 0.04263526 0.379513854 -0.157687296 -0.1220727 -0.04305240 0.07266218 -0.007533977 0.14634095 0.25658376 0.45865011 -0.07414341 0.08676525 0.2972831 0.20881219 0.005408232 0.28084413 -0.11613621 0.17679797 0.32776928 0.01952200 -0.12391902 -0.24619662 0.49886083 -0.02607648 -0.001236969
oligodendrocytic_up 0.23276809 0.1579273 0.27834655 0.16541114 0.2967757 0.20073958 0.05308861 0.16548555 0.2960602 -0.06212319 0.2511061 0.23363850 0.49638543 0.20198656 0.02902960 0.30191162 -0.09088903 0.17653174 0.2923147 0.173427872 0.233041698 0.12377225 0.2739099 0.17169148 0.36533533 0.30762144 0.395886181 0.210670157 0.3295785 0.20726009 0.20552805 0.352208428 0.23866032 0.36220935 0.33072346 0.38151672 0.10382195 0.2867132 0.40519888 0.104315543 0.27453019 0.08890069 0.02961855 0.35470642 0.42481129 0.14658324 0.13577067 0.21517457 0.09820911 0.073203757
TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up -0.12781345 -0.10424801 -0.003896955 0.23387421 0.25246844 0.3207035 0.1864102 0.2276360 0.264613462 0.16772316 0.1921236 0.150618790 0.2158142 1.480129e-01 0.2547912 0.2467531 0.16111355 0.19983249 0.07535168 0.28372256 0.14028380 0.14573966 -0.04131919 0.09047686 0.1447905 0.10384463 0.174769701 0.15962850 0.23867927 0.147562489 0.17203901 0.32877500 0.12467503 0.2831480 0.21697481 0.2582061 -0.04827454 0.070849773 0.10375364 0.05993822 0.14917783 0.03705593 0.28737667 0.1128391 0.15477895 0.16409778 0.143848674 0.08997557 0.25033466 0.200997387
astroglia_up -0.33567021 -0.09558514 -0.267132320 0.27697125 0.04553025 0.1866003 0.1084145 0.1548024 0.115683387 0.08879166 -0.1794232 0.005649495 -0.1576545 -1.257789e-05 0.0727411 0.1555954 -0.05570396 0.07701213 -0.20774164 -0.04776384 0.13345907 0.02623989 -0.02663276 -0.05953059 -0.1011001 0.02571005 0.182406879 0.02375654 0.06349979 0.063565080 -0.03836509 -0.03293448 -0.03572666 0.1665919 0.16071904 0.2015802 -0.03462372 0.294133704 0.07912455 -0.09833367 -0.01426256 0.25177173 0.13323749 0.2085587 0.11625433 0.09270277 0.061118313 -0.01415236 0.09864426 -0.067173534
neuronal_up 0.07027706 -0.02131532 0.238480842 0.38752317 -0.15659472 0.3577991 0.1892366 0.5672812 0.353841822 0.17010487 0.6047937 0.354282079 0.6087488 1.055863e-01 0.1732358 0.4886717 -0.06147035 0.24909699 0.54129393 0.09127180 0.05607375 0.28403989 0.41755055 -0.07975270 0.5899966 0.33505856 0.102693909 0.28051577 0.08310426 -0.006844963 -0.31495393 0.26595406 -0.30096794 0.4279460 0.10930434 -0.2523735 -0.27065562 -0.331425847 -0.04027485 -0.13510844 -0.02925798 -0.13647458 -0.06576075 -0.1651269 -0.23599409 0.08160665 -0.024158946 -0.39125116 -0.08528125 0.242973089
oligodendrocytic_up 0.26340390 0.20728662 0.238562146 0.03463889 -0.23287645 0.1609936 0.1784241 0.2769686 -0.005855304 0.17838346 0.2103914 0.079351508 0.1988334 1.691518e-01 0.1326108 0.2505812 -0.04892868 -0.03712413 -0.06713938 0.01717354 0.34941440 0.14144163 -0.01200277 0.09049891 0.2205388 -0.16470176 0.007669828 -0.08375967 -0.07398330 -0.023669180 -0.06730557 0.04221507 -0.02535599 -0.1434455 0.04683426 0.1519900 -0.01026107 0.006264224 -0.09514740 -0.09808242 -0.10883555 -0.08778694 -0.07144261 -0.1419069 0.01198113 -0.08184800 -0.006479715 -0.04310793 0.03696027 -0.009964341
TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up 0.23574567 0.27008722 0.11637555 0.16765565 0.1642266 0.03292988 0.2114207 0.13123819 0.2632937 0.255558714 0.12614825 0.22137032 0.16832484 0.2957996 0.2482320 0.20144142 0.29253731 0.3005284 -0.0101724 0.23305725 0.04509015 0.009178942 -0.001041475 0.2798335 0.03802142 0.055982875 0.10438785 0.05182689 0.10224425 0.05216468 0.0862304 0.02155929 -0.003172836 0.06739361 0.06256693 0.26367322 0.11536744 0.01256467 -0.01613898 0.09388852 0.11605589 -0.022074828 0.01870171 0.1159158 0.06165079 0.1766942 0.16406312 0.1409899 0.1558032 0.1268423
astroglia_up 0.08497700 0.03829140 0.30608201 0.15711765 -0.1874617 -0.03283596 0.2290560 0.24698566 0.1847376 0.003580519 0.05081910 -0.04184080 0.23607570 0.1738209 0.1859548 0.11158631 0.02925080 0.2737893 0.3973568 0.25676961 0.39896998 0.362511205 0.397819214 0.3570748 0.25126109 0.160334429 0.40718110 0.34688248 0.36362766 0.26827732 0.3482736 0.31181324 0.269671812 0.31453886 0.29877113 0.44352730 0.40788910 0.14601178 0.31162191 0.29587323 0.37947936 0.349232664 0.33243016 0.2628245 0.34952493 0.2376603 0.14605626 0.3990569 0.3289481 0.2267814
neuronal_up 0.28985543 -0.22610913 -0.06872989 -0.35634904 0.2051659 -0.15883492 -0.1861080 -0.17803520 0.1460343 0.105040208 -0.04944198 -0.33779090 0.29735931 -0.2133380 -0.3174639 -0.16643769 -0.20111679 -0.1413125 -0.1650908 0.01813617 -0.10455488 -0.296484567 -0.187537508 0.2442998 -0.07725316 -0.066574793 0.08146431 -0.06163985 -0.33529820 -0.25395066 0.2275310 0.48981934 -0.150285119 -0.09120100 -0.16014135 -0.01354999 -0.07519059 0.19440942 -0.18040416 -0.21007375 -0.10276626 -0.141371655 -0.21314137 -0.1962376 -0.14976707 -0.1246511 -0.17372631 -0.2207284 -0.1757595 0.1906853
oligodendrocytic_up -0.04365214 -0.01038323 -0.06776547 -0.08472649 -0.1248816 -0.16991651 -0.1094051 -0.06642471 -0.2030105 0.013242268 -0.01680738 -0.03299205 -0.08840665 -0.2023591 -0.0859446 -0.06875004 -0.09073745 0.4037900 -0.0373881 0.12233991 0.07562161 -0.047601068 0.128217901 0.0132698 -0.15651784 0.007475202 -0.04953692 -0.13635011 -0.02535448 -0.07229950 0.1823742 0.37025576 -0.057417938 -0.06801955 -0.05093462 0.09347360 0.14824246 0.18023574 0.43900131 0.01998225 -0.04886937 -0.003561142 0.12171143 0.2173272 0.20198714 -0.2138286 -0.04280936 -0.1078011 0.2334409 0.1350531
TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up -0.01384884 0.1922211 0.1338636 0.11847725 0.1641095 0.006294324 -0.008137892 -0.13724891 0.2054020 0.12997632 0.01119348 0.05979755 0.1010092 0.08196094 0.06026906 -0.000531532 -0.04216870 0.04782013 0.13415875 0.1741715 -0.04346128 -0.02707061 0.0641008
astroglia_up 0.25182230 0.2092300 0.3504668 0.38080141 0.3572364 0.285424310 0.266573973 0.21241946 0.3210299 0.26738072 0.31228683 0.39524758 0.3530827 0.36410787 0.42455013 0.259007098 0.19900055 0.21611551 0.25564425 0.4072161 0.27182445 0.30879011 0.2296599
neuronal_up -0.21981790 -0.1745162 -0.1645862 -0.16331593 -0.1907196 -0.148526527 -0.150903069 -0.20298432 -0.1494018 -0.31979492 -0.07684811 0.12502843 -0.1325836 0.39917847 -0.26476090 0.306810092 -0.03434656 0.11584141 -0.25353924 -0.1629485 -0.11841551 -0.26324244 -0.1689706
oligodendrocytic_up 0.01801927 0.1762533 -0.1216974 -0.02033394 -0.1266508 -0.086965414 0.006808870 -0.05324112 -0.0283358 -0.08040521 -0.01867919 0.07793677 0.1875986 -0.10327650 -0.02771945 0.087825011 -0.13564146 -0.08870616 -0.02615045 -0.0209192 -0.07626177 -0.05744868 0.1065117
>
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> leukPar <- ssgseaParam(leukemia_eset, cgpC2BroadSets,
+ minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP -0.11212188 -0.09106815 -0.121150864 -0.08143375 -0.088090518 -0.07340947 -0.10376635 -0.12329046 -0.107490316 -0.1094321479 -0.09602253 -0.097841141 -0.052252012 -0.107114347 -0.10907601 -0.07366425 -0.12469120 -0.105311438 -0.11210642 -0.07831097 -0.095506069 -0.09272797 -0.080016602 -0.0601701101 -0.086388455 -0.086143328 -0.07964313 -0.07476053 -0.11573733 -0.106800817 -0.07058489 -0.083557328 -0.08462769 -0.090099523 -0.0549047537 -0.104821669 -0.12270687
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP 0.12773870 0.11958013 0.169039831 0.08039046 0.079764086 0.04745847 0.17432542 0.10197508 0.108268340 0.2006370201 0.12760627 0.136610607 0.094614756 0.075754012 0.13272714 0.10349286 0.08997838 0.105152129 0.07972599 0.04842713 0.156201488 0.10861902 0.048660863 0.0486013305 0.094428151 0.067025764 0.07166594 0.02581748 0.01906544 0.053825100 0.11114079 0.146989381 0.08036877 0.070876416 0.1065750807 0.032006331 0.03126135
WINTER_HYPOXIA_UP 0.19660336 0.22220588 0.208150808 0.20369715 0.194220520 0.18637683 0.18791267 0.18394723 0.191934075 0.2073623135 0.18961007 0.206889571 0.227895816 0.218581670 0.19144735 0.22310948 0.19439608 0.202960622 0.20949776 0.19542339 0.216907511 0.24031950 0.208217532 0.2011029977 0.234533054 0.221475821 0.19919427 0.23800347 0.20715801 0.230102555 0.24544630 0.211888487 0.22075250 0.213354811 0.2209719414 0.212552165 0.19720964
PYEON_HPV_POSITIVE_TUMORS_UP 0.12936217 0.08608186 0.156095439 0.04512521 0.100883198 0.11208812 0.12352973 0.17187068 0.153348975 0.1703012802 0.11051421 0.170675622 0.015252592 0.094679684 0.14160524 0.08032573 0.13750853 0.138672606 0.08985131 0.03661538 0.105799747 0.08113882 0.107166119 0.0506252281 0.047816290 0.095272447 0.10133515 0.08434566 0.11544536 0.046634453 0.06811758 0.136585794 0.09329885 0.066439827 0.0424873211 0.055346301 0.11044267
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP 0.10497861 0.11810250 0.130550079 0.08824334 0.067996562 0.09001761 0.10880848 0.09112328 0.114928671 0.1341928379 0.11162537 0.121156220 0.097889549 0.134823238 0.11398214 0.10943782 0.10538109 0.110901558 0.10004585 0.07652972 0.124448823 0.09605908 0.095401105 0.0800272992 0.125435027 0.107655114 0.07785774 0.11689738 0.10900193 0.126404590 0.13500916 0.118357443 0.12482627 0.132783820 0.0875660360 0.100749901 0.08896426
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP -0.14415962 -0.13112123 -0.148059446 -0.13794539 -0.137336129 -0.12385178 -0.12980927 -0.14141721 -0.145591804 -0.1413958552 -0.11800610 -0.144207294 -0.131972015 -0.141042585 -0.12498393 -0.14357730 -0.12949535 -0.154721081 -0.14240748 -0.12956549 -0.143591188 -0.13236731 -0.149298176 -0.1300145478 -0.131174376 -0.136769869 -0.12031729 -0.13417144 -0.14801656 -0.103740991 -0.11897875 -0.131464086 -0.12259302 -0.128755678 -0.1259053782 -0.135984581 -0.13075821
LU_TUMOR_VASCULATURE_UP -0.08611663 -0.03840696 -0.075208780 -0.06571226 -0.059283399 -0.09743345 -0.01241906 -0.11715637 -0.095094587 -0.0942931758 -0.04907607 -0.091230456 -0.074117889 -0.052525843 -0.06551791 -0.04611678 -0.06288770 -0.095388286 -0.05466379 -0.02196421 -0.089002940 -0.02903084 -0.099934618 -0.0328273529 -0.059930837 -0.093726300 -0.06905892 0.03385055 -0.10159676 0.062777131 -0.04579346 -0.064021288 -0.02096713 0.041382070 -0.0659072134 0.004541717 -0.08085065
KORKOLA_EMBRYONAL_CARCINOMA_UP 0.14802750 0.19989559 0.193531409 0.19043055 0.164415884 0.14670572 0.13835951 0.15782717 0.158620695 0.1923823767 0.17142120 0.191193516 0.189426831 0.200421860 0.17161690 0.21494495 0.18205192 0.192282258 0.16595727 0.17568860 0.212460788 0.19870684 0.195131434 0.1589439546 0.191376696 0.173976522 0.15799413 0.19036604 0.19127428 0.176196755 0.18543632 0.176852454 0.19522737 0.136840003 0.1714436876 0.171497790 0.18616571
KORKOLA_TERATOMA_UP 0.22823416 0.29024180 0.231155370 0.23171935 0.254748989 0.19408563 0.16835792 0.16188829 0.112118254 0.1565428797 0.20383020 0.123476972 0.217612011 0.244082034 0.22362179 0.28040203 0.20831738 0.168287700 0.24110595 0.23418356 0.244983055 0.25692773 0.200311939 0.2184469742 0.248702703 0.190689786 0.21178104 0.22717410 0.21281765 0.198438514 0.21014560 0.161257116 0.19694428 0.158841418 0.2076681127 0.196667083 0.21540144
KORKOLA_YOLK_SAC_TUMOR_UP 0.34466298 0.39892106 0.377886303 0.33108088 0.355059703 0.34014296 0.33424236 0.33551668 0.322514107 0.3587143377 0.35616777 0.345656031 0.361905734 0.356409761 0.34356338 0.36466181 0.35676080 0.353135417 0.34782607 0.35557146 0.369519925 0.37855110 0.340752613 0.3310743436 0.310692783 0.333271917 0.33092650 0.35381284 0.34636036 0.330627105 0.35041188 0.339198683 0.36176745 0.298834876 0.3344121129 0.355416500 0.34180114
KORKOLA_CHORIOCARCINOMA_UP 0.44015614 0.48855227 0.450504964 0.46641488 0.448745786 0.41967427 0.40468719 0.44145971 0.455353414 0.5056625648 0.49198361 0.489745578 0.490534332 0.483410654 0.48684370 0.50623699 0.50398811 0.496025889 0.46027781 0.48204686 0.502594106 0.49342943 0.461528278 0.4453763188 0.453555580 0.457458981 0.44222231 0.48845097 0.47883248 0.485213780 0.48703015 0.459726900 0.46124201 0.434116406 0.4887206089 0.467923068 0.49059426
KORKOLA_SEMINOMA_UP 0.13847750 0.17850772 0.174597045 0.16508981 0.157223586 0.15596102 0.14187743 0.14411233 0.155857399 0.1758869779 0.17913681 0.168367099 0.161656280 0.177625715 0.15933775 0.16766991 0.17459358 0.187638049 0.16053712 0.18068610 0.160177064 0.16297719 0.143814313 0.1368714657 0.146708281 0.137036347 0.13672037 0.16405538 0.15687579 0.149515564 0.15499412 0.151293558 0.16531883 0.125764891 0.1551887231 0.172244543 0.16315928
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP 0.27744218 0.26350935 0.297888085 0.25976966 0.276608184 0.25693663 0.27761830 0.28848813 0.286664487 0.2762852086 0.27840239 0.291426599 0.282808179 0.294631962 0.29385340 0.26740892 0.28461746 0.296478631 0.29646299 0.26712951 0.297136943 0.29037251 0.290182379 0.2766321689 0.294832624 0.290120635 0.28546834 0.29985442 0.31836713 0.295872223 0.25619716 0.283982155 0.29792700 0.299964305 0.2675484590 0.301101215 0.29995819
HOLLMAN_APOPTOSIS_VIA_CD40_UP 0.20838568 0.20620590 0.226021285 0.18903855 0.205996318 0.21204142 0.21967797 0.21308316 0.201127727 0.2021400473 0.20717155 0.215017814 0.187117852 0.219969815 0.21173231 0.19604622 0.21329915 0.212552604 0.19626079 0.19827681 0.211735913 0.19112536 0.203069987 0.2197126547 0.197947624 0.204388551 0.19946042 0.20608121 0.21291368 0.212708378 0.19862400 0.209122222 0.19925121 0.211899137 0.1938569725 0.222442050 0.21241407
LIU_PROSTATE_CANCER_UP 0.12333806 0.12822475 0.122836081 0.12725808 0.140594244 0.12825347 0.11034224 0.11649062 0.120184024 0.1301693730 0.12229130 0.129704667 0.137069254 0.111577549 0.11871748 0.11882426 0.12222041 0.139520829 0.11722272 0.12381120 0.128360065 0.13208683 0.142162149 0.1356536483 0.114693190 0.133318936 0.13748781 0.12832984 0.11667838 0.122081679 0.13437113 0.135333521 0.14198109 0.117064049 0.1415429031 0.128631348 0.11727950
LIU_SOX4_TARGETS_UP 0.08191204 0.05214134 0.096757396 0.07523797 0.079421912 0.07708861 0.08083627 0.10566201 0.079132766 0.0800895023 0.09502955 0.065630075 0.033165065 0.070986201 0.10605029 0.08258342 0.08768873 0.071996983 0.11390213 0.09018520 0.065872711 0.02685959 0.066144677 0.0727056296 0.082403808 0.073595763 0.06589577 0.06643292 0.09747230 0.106162263 0.04897972 0.066492306 0.06313290 0.112840981 0.0424372639 0.065643621 0.10517315
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP 0.12962537 0.11610080 0.145466087 0.12133965 0.151001465 0.12542172 0.12193757 0.11684710 0.124876198 0.1227735670 0.12962045 0.133337998 0.145216907 0.141828051 0.15001820 0.13815100 0.13460255 0.151878290 0.13727416 0.15746327 0.139912030 0.13476324 0.129655986 0.1284177003 0.132525587 0.130459851 0.12869022 0.13923393 0.13259415 0.155502893 0.13899383 0.126465783 0.14275177 0.146336368 0.1220863251 0.171552323 0.12417440
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP -0.04699784 -0.03856334 -0.028301448 -0.03891271 -0.045089149 -0.03704312 -0.02630941 -0.02816459 -0.029559739 -0.0534978383 -0.01366122 -0.041830107 -0.050639545 -0.040411674 -0.02102565 -0.03970615 -0.01799213 -0.033341689 -0.01897268 -0.01365414 -0.028107224 -0.02713442 -0.046683538 -0.0206629560 -0.018977519 -0.038659175 -0.03223894 -0.01494866 -0.02004138 0.028290459 -0.02212699 -0.038100635 -0.02119184 0.003239358 -0.0369081395 0.014342415 -0.01112552
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP -0.09394028 -0.10883789 -0.125696986 -0.07648813 -0.114219799 -0.09129576 -0.10820034 -0.09787250 -0.092631165 -0.0637997483 -0.07766220 -0.094268793 -0.082937625 -0.106384923 -0.08192685 -0.10758882 -0.08542658 -0.092203040 -0.06488157 -0.09003358 -0.111067169 -0.08970828 -0.114620536 -0.0850125408 -0.059028109 -0.122409700 -0.11287838 -0.08916244 -0.09472273 -0.077911670 -0.09390619 -0.097644568 -0.11001932 -0.078106059 -0.0940344476 -0.091955745 -0.07766899
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP 0.02510931 0.08834848 0.080971697 0.01114658 0.025264412 0.04515388 0.06017182 0.06139166 -0.001637575 0.0902450722 0.02735733 -0.004243082 0.008884452 0.024612352 0.02882780 0.04029161 0.10199346 -0.025891095 0.01797175 0.03194774 0.099164270 0.07272077 0.001372288 0.0386279383 0.018516022 -0.003201053 0.04261062 0.04512323 0.05409370 0.082268487 -0.01156691 0.038932474 0.05063402 0.046801355 0.0762341100 0.031483923 0.09146968
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP -0.01159980 0.01773789 0.002741870 0.01471238 -0.003972485 0.01295277 0.02605081 0.02748918 0.012317275 0.0001521724 0.01504880 0.002445162 0.026606924 0.001673537 0.04936615 -0.01373036 0.01157459 -0.001213928 0.02950728 0.02709116 -0.001369139 0.01070392 -0.008326614 0.0005865785 -0.006947417 0.003683486 0.01476815 0.00833425 -0.02602648 0.005669794 0.02372157 -0.002592865 -0.01080445 0.018411711 -0.0002326556 -0.019837822 -0.02111218
FRASOR_TAMOXIFEN_RESPONSE_UP 0.06343555 0.06524186 0.076096149 0.08623646 0.035901095 0.05553414 0.04813651 0.05000595 0.018630799 0.0361654200 0.04294741 0.045994056 0.084165291 0.039521918 0.04147761 0.03215540 0.04010818 0.043314016 0.07676386 0.04559031 0.070087913 0.07091543 0.059398083 0.0706534110 0.071532990 0.068066629 0.06426931 0.07338332 0.08518933 0.065149663 0.07183749 0.066367920 0.06594029 0.077125008 0.0927989288 0.074142612 0.07559066
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP 0.03004809 0.05432805 0.001432391 0.02459771 0.011252625 0.04038848 0.02972862 0.01314790 0.002092703 -0.0156113936 0.04748579 -0.011117702 0.009640799 0.033918561 0.03840938 0.04608757 0.01172223 -0.005214653 0.03919416 0.04798752 -0.003693506 0.02843361 0.014212574 0.0239450749 0.022041404 0.002291239 0.03366971 0.04054535 0.02752102 0.053112241 0.05954476 0.008942285 0.01327435 0.032914846 0.0378134578 0.024061336 0.01399793
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP -0.03953071 -0.05465739 -0.007602480 -0.09969782 -0.064649394 -0.07536982 -0.04164320 -0.05312600 -0.043319892 -0.0119909722 -0.05473042 -0.040898014 -0.087901954 -0.049785859 -0.01812754 -0.08046669 -0.04513855 -0.042191116 -0.06131214 -0.08200335 -0.042998833 -0.05742151 -0.078783092 -0.1056325522 -0.069303843 -0.057059264 -0.07539755 -0.06329446 -0.06679513 -0.049903218 -0.05732776 -0.036949074 -0.04247288 -0.046862641 -0.1023930938 -0.071387634 -0.08894461
WATANABE_COLON_CANCER_MSI_VS_MSS_UP 0.04819844 0.08558284 0.055708783 0.10324646 0.050709634 0.04995449 0.04822270 0.03763487 0.066913831 0.0260843037 0.03852020 0.041160906 0.092662161 0.050620558 0.03429650 0.05177460 0.08589703 0.046940975 0.04818196 0.04030422 0.077704576 0.10913606 0.057248585 0.0744440801 0.078206610 0.092934179 0.05650890 0.06626172 0.06222949 0.035216390 0.08404366 0.042016648 0.04474503 0.077050552 0.0877448713 0.057929757 0.02811160
>
> proc.time()
user system elapsed
66.62 5.25 70.35
GSVA.Rcheck/tests/test_ssgsea_newapi.Rout.save
R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> ## 2023-11-10 axel: simple test script for method ssGSEA, new API
>
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
expand.grid, I, unname
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db
> library(GSVA)
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 1.4171739 -1.3444519 -0.99052898 0.4203395 1.30716224
g2 -0.7281951 0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754 0.09779699 -0.6792548 -0.09124045
g4 1.0735382 1.3156255 0.15588330 -1.8079608 0.48531108
g5 0.7229884 -0.9162342 1.93982245 0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> ssgseaPar <- ssgseaParam(X, gs)
> ssgsea.es <- gsva(ssgseaPar, verbose=FALSE)
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> dim(ssgsea.es)
[1] 100 30
> ssgsea.es[seq.int(min(nRowsToPrint, nrow(ssgsea.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 0.050046308 0.153445680 0.06440230 0.245928762 -0.039281351 -0.009166497 0.15513670 0.05825828 0.075703720 0.2211977472 0.1909755963 0.213798011 -0.061198758 0.067211285 0.14116126 0.172193009 -0.076107078 0.146208482 0.27199640 0.027375283 0.25958081 -0.106935451 0.01955332 0.31199267 0.18689996 -0.02538041 0.025160949 0.10202723 0.317960731 -0.077195317
gs2 0.081171485 0.161930448 0.19635614 0.226977722 0.084705475 0.122712065 0.25375216 0.06124718 0.245645786 0.0213152908 0.1553307677 0.123198146 0.188559702 0.090605381 0.13634300 0.045583205 0.117061823 0.170602582 0.25518183 0.162276466 0.09782367 0.004672292 0.14429067 0.23905295 0.15842119 0.17958482 0.278174676 0.12969068 0.012534148 0.036195649
gs3 0.155539308 0.008842632 0.17903935 0.114060106 0.107208758 0.184963019 0.11327060 0.17081118 -0.110611530 0.3187327429 0.0896885519 0.169232189 0.292515661 -0.109522283 0.39211201 0.036070929 0.141878189 0.192157970 -0.01831034 -0.028374783 -0.31739185 0.238016028 -0.06330888 0.16972085 0.38536400 0.19915210 0.020583043 0.25012966 0.186034734 0.232849532
gs4 0.100407452 0.178458402 0.10660518 0.159340098 0.150690547 0.242066049 0.09044728 0.13980211 0.072737831 0.1082857648 0.0915659224 0.136234969 0.061324248 0.115973559 0.28107234 0.138134111 0.214028524 0.086667572 0.09385724 -0.029785545 0.12586634 0.082632971 0.17808866 0.21133946 0.16632346 0.17155219 0.102324377 0.20705832 0.099089588 0.290472119
gs5 0.194033575 0.062793781 0.04848598 0.217341759 0.191914352 0.129512577 0.15090606 0.27146643 0.219627621 0.1165628347 0.1379487730 0.152302042 0.099901051 0.205679023 0.12986947 -0.004963142 0.190709801 0.174401755 0.04427775 0.082055507 0.10896263 0.068825475 0.07614058 0.13558182 0.10568477 0.11492927 0.188047631 0.14065184 0.172431746 0.144376505
gs6 0.025988630 0.233512601 0.04485374 0.149671413 0.164451696 0.223396448 0.13735451 0.15303178 0.125071887 0.2456561342 0.1220311380 0.059904884 0.034633361 0.006225782 0.14294390 0.105914640 0.118989560 0.234603796 0.05542837 0.175273940 0.12454592 0.055488242 0.25878309 0.07422275 0.08197481 0.27581388 0.111785007 0.10024739 0.028180564 0.147366318
gs7 0.121579155 0.248146053 0.20935405 0.098421904 0.005775149 0.141790217 -0.04190763 0.02191384 0.225359966 0.0003605319 0.1938341367 0.218166804 0.234711429 0.171511561 0.14870761 0.004943158 0.168428297 0.131664402 0.16148235 0.046908832 0.09016756 0.199893820 0.17366414 0.10055547 0.08930753 0.16771471 0.141067369 0.20184683 0.113755713 0.062537548
gs8 0.175951236 0.104036859 0.16715411 0.066581368 0.124736570 0.107121162 0.15227018 0.13551209 0.066044097 0.0704654595 0.2006164228 0.164797947 0.149994634 0.063391557 0.20349135 0.205315802 0.006936426 0.130049520 0.17910706 0.061817683 0.05195776 0.059676074 0.18475605 0.10873217 0.25833265 -0.05691274 0.152978263 0.16063583 0.115089785 0.086840652
gs9 0.012967426 0.095461238 0.31825984 0.426422393 -0.206013607 -0.324946275 0.08738730 -0.14420537 0.061606991 0.1058375433 0.3407494698 0.060782012 0.036354426 0.158643593 0.02660000 0.070018029 0.295526014 0.370485869 0.31177819 -0.048490861 0.14293901 -0.052155641 0.39443397 0.18784912 -0.02491664 0.42956908 0.004366843 -0.09351215 0.539660825 0.194470958
gs10 0.310450557 -0.155381634 -0.04662343 0.069903089 0.235460838 0.136094565 0.35534293 0.14451145 0.032811542 0.2783927322 -0.0003708892 0.364801135 0.085153930 -0.007025257 0.31541487 0.214116068 0.076379415 0.300464786 0.02436326 0.014174550 0.29010030 0.353773500 -0.14036272 0.31414362 0.07517937 -0.36240056 0.135363804 -0.03291463 0.153638245 -0.006111044
gs11 0.148113831 0.288039198 -0.01173447 -0.125211500 0.422877496 0.368992470 0.31511056 0.11703945 0.119067901 0.2969431165 0.1767112563 0.269003140 -0.126699232 0.063371585 -0.15584600 -0.181509478 -0.252102260 0.084592131 0.41484382 0.102741674 0.19038088 0.155665264 0.11205065 0.18151841 0.07962262 -0.12707952 -0.043348625 0.52382483 0.471772841 0.192133037
gs12 0.191362265 0.075821020 0.10101534 0.015589766 0.118539915 0.150230064 0.11740963 0.09874133 0.196307720 0.1336100372 0.2243542624 -0.037860476 0.035827902 0.019570602 0.05739397 -0.086404343 0.090407547 0.090844017 0.11188849 0.250652019 0.15642076 0.100960304 0.13217523 0.09147595 0.14935140 0.07679723 0.164747489 0.10884565 0.021875796 0.224835781
gs13 0.291858703 0.346475308 0.21825672 0.130219327 -0.045991328 0.234867271 0.34027295 0.11127727 0.246617815 0.3200429439 0.0493766799 0.008390396 0.100929397 -0.036222987 0.09552925 0.116070504 0.050409473 0.117373720 0.33645267 0.196460577 0.28151964 0.250645402 0.00786962 0.16471272 0.26987750 0.14003078 0.274510723 -0.06972362 0.111250445 0.031727494
gs14 0.190335262 -0.064441167 -0.14720764 0.313073121 0.184851969 0.034311372 0.29316721 -0.12497882 0.099774835 0.0064937265 0.1376061089 0.105283947 0.322046351 0.260972829 0.22468693 0.113901307 0.002316888 0.174550489 0.03848764 0.149291379 0.16606614 0.171358521 -0.23264680 0.06333781 0.26046384 0.14647155 0.061583955 0.07893101 0.084042439 0.241795872
gs15 0.217913642 0.141978343 0.21703088 0.061088530 0.048906153 0.109096881 0.04362714 0.21225573 0.180978230 0.1203085545 0.0888328589 0.183656898 0.074251458 0.108846516 0.01790968 0.222984303 0.115016738 0.124120115 0.11555410 0.162960343 0.12134445 0.108547160 0.18775900 0.20267430 0.21813681 0.05956895 0.081086983 0.04401661 0.004584748 0.113053205
gs16 0.008372193 0.198823477 0.02924146 0.187858615 0.054689339 0.068398317 0.10730408 0.05120743 0.070935563 0.0784796201 0.0060339391 0.097386464 0.181367848 0.060028026 0.18405253 0.129145564 0.127244708 0.083034338 0.06835057 0.111075315 0.12519485 0.101386193 0.10027865 0.07630206 0.11786623 0.12151097 0.076099407 0.06340149 0.199302468 0.107472386
gs17 -0.021209113 0.041234441 0.15849782 0.140830687 0.094989136 0.050310553 0.27875609 0.19671686 0.224090634 0.0823059119 0.1446622842 0.073610528 0.181135843 0.128995630 0.18515033 0.043619934 0.156832276 0.139817243 0.12097998 0.094078972 -0.01250999 0.263313353 0.18157262 0.06476920 -0.02611791 0.19436554 0.098776218 0.15857389 0.086521226 0.140174046
gs18 0.224221766 0.208703330 0.19566999 0.277362679 0.086022967 0.155782407 0.21984017 0.06224476 0.184311430 0.0746810884 0.1500112520 0.031591001 0.218220154 0.085782290 0.05403013 0.239733411 0.225608272 0.080410483 0.12419147 0.087988742 0.09109210 0.118154979 0.18042347 0.15034333 0.05419059 0.06131728 0.135992696 0.05116987 0.008007108 0.258350779
gs19 0.060496086 0.192359984 0.06580294 0.039342129 0.056421351 -0.050071255 0.09835605 0.19838255 0.232365057 0.1878213634 0.0597175977 0.113955441 0.138654652 0.118112400 0.02948580 0.183873151 0.295382463 0.084940527 0.01555718 0.237711415 0.15405004 0.113893226 0.01261294 0.08150703 0.13679835 0.17664342 0.264724147 0.09871800 0.219093664 0.229287431
gs20 -0.002331868 0.104835345 0.19095558 0.196525176 0.230511428 0.196485997 0.20691704 0.06292261 0.195484717 0.0748935120 0.2274655731 0.234958644 0.100720547 0.098787011 0.01322616 0.215826190 0.107383744 0.272734953 0.14006653 0.128606660 0.17526232 0.154071267 0.20185690 0.16029505 0.11767405 0.04019989 0.087560954 0.12297014 0.120555888 0.165784444
gs21 0.235531812 0.174101071 0.04331386 0.066700909 0.161550174 0.127508845 0.22978825 0.07748909 0.142407170 0.1262273951 0.0698341132 0.023900707 0.157264078 0.064306708 0.19037040 0.022272735 0.085059711 -0.030333898 0.10370986 0.041024634 0.15543738 0.156630569 0.11755610 0.14827641 0.09418257 0.26082349 0.175064303 0.10818015 0.134571164 0.137789233
gs22 -0.047650929 0.186841315 0.03222656 0.119471610 0.193877261 -0.031790084 0.29277495 0.07689763 -0.019411157 0.0595495594 0.3807452330 0.071668171 0.135528037 0.177342300 0.18766862 0.143986114 0.138391599 0.137573467 0.11420368 0.222882426 0.06096151 0.160136193 0.37542340 0.34681913 0.02224170 0.20670334 0.053159207 0.38290841 0.093613064 0.168206100
gs23 0.144199311 0.186850465 0.09563174 0.191503633 0.197926948 0.183687676 0.08857992 0.08438396 -0.002354026 0.1015861893 0.1556606664 0.149031544 -0.003876439 0.220881227 0.19108193 0.128779302 0.115583034 0.128810013 0.21233978 -0.001768056 0.13275623 0.154387029 -0.06742232 0.07991395 0.15197278 0.23716849 0.161038324 0.06541124 0.045781546 0.096529440
gs24 0.244519906 0.255495479 -0.02212643 0.007561398 0.045577309 -0.009892961 -0.04971968 0.19698687 -0.078933887 0.0414502136 0.3742714753 -0.050544352 0.013590683 0.003608241 -0.34825490 0.415098155 0.138025957 -0.001864139 -0.37016901 0.117420895 0.37252626 -0.116751635 0.32072205 -0.06702968 0.11533867 0.21077948 -0.041474525 0.03217032 -0.044872621 0.165434542
gs25 0.193601681 0.091245208 0.18463093 0.100724310 0.055381436 0.002669872 0.08514397 0.05620041 0.124029775 0.1800670374 0.1742834586 0.170840558 -0.034319609 0.177918537 0.09381717 0.145284931 0.208953543 0.324830001 0.16350519 0.037554150 0.26681356 0.012083285 0.28774452 0.13816374 0.05451236 0.10453580 0.280375699 0.12512785 0.135834785 -0.038267879
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+ grep("^REACTOME", names(c2BroadSets)),
+ grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- ssgseaParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+ minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.21698978 0.190101718 0.20525435 0.21623854 0.228779757 0.20936853 0.22506971 0.2234235687 0.220780261 0.21444921 0.21903592 0.220664804 0.20924941 0.21012248 0.20502111 0.19985724 0.19721755 0.1913957094 0.225134348 0.21709921 0.20425590 0.201712948 0.19379346 0.23122161 0.221525326 0.212463371 0.22792181 0.221128254 0.204351144 0.218947974 0.222579602 0.229420498 0.22060750 0.20299621 0.21904369 0.215493102
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.32433043 0.330666662 0.31869186 0.30766734 0.322670342 0.31519248 0.31986814 0.3185006606 0.329706974 0.31265435 0.32676917 0.331734849 0.31520463 0.32288700 0.31043279 0.31220717 0.30722070 0.3168181879 0.320522995 0.32920820 0.31023554 0.313528956 0.32324416 0.32442285 0.307746225 0.302000352 0.31422539 0.325061712 0.324433443 0.320805701 0.313120479 0.322340322 0.32303440 0.31470507 0.32982874 0.322774682
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.32613456 0.292246085 0.32171779 0.31922331 0.327342371 0.32285413 0.31703691 0.3267972444 0.317799481 0.30548746 0.32071494 0.325200548 0.31574521 0.32222525 0.30445849 0.31198274 0.30056356 0.3175363433 0.313248908 0.31537383 0.31498239 0.312138133 0.31157241 0.31348063 0.313260085 0.305543436 0.31306655 0.318602720 0.309415331 0.316959102 0.307805386 0.319474001 0.30318847 0.31470071 0.31941053 0.326759498
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.14142675 0.152207936 0.14238572 0.07942752 0.105050011 0.12961280 0.11296245 0.1601888948 0.141345242 0.09869492 0.16412075 0.158434716 0.10823031 0.17672793 0.13428568 0.11392145 0.14170168 0.1428868433 0.146955737 0.14818936 0.17164951 0.138839694 0.12229281 0.11673825 0.109550600 0.069456602 0.14040696 0.182050959 0.114699787 0.189319064 0.130300608 0.111638487 0.14391952 0.12318954 0.12224946 0.137976483
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.15550203 0.118146628 0.14707933 0.18705703 0.199943713 0.16410186 0.16813615 0.1802125060 0.170259262 0.18671240 0.18252531 0.164279928 0.16794179 0.17149276 0.16625970 0.14528892 0.13398404 0.1378452121 0.169092878 0.19220147 0.19047757 0.157694632 0.12722729 0.18630354 0.195343439 0.176599720 0.19802720 0.161573744 0.152184181 0.173797461 0.187295272 0.197591583 0.17232864 0.16136207 0.17911558 0.180031024
KEGG_GALACTOSE_METABOLISM 0.11149473 0.103217880 0.11085844 0.13741766 0.165952026 0.14418332 0.12726683 0.1370210459 0.142805283 0.15242781 0.15221252 0.149682255 0.15018345 0.14626213 0.11999955 0.11557928 0.11593006 0.1148701557 0.149672283 0.16891575 0.16494312 0.123919369 0.09211866 0.14937665 0.176575543 0.129061875 0.17075453 0.137859374 0.112830567 0.139888692 0.144650768 0.159081145 0.13428014 0.12448791 0.15631215 0.169827420
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.04198555 -0.032292278 0.01406413 -0.01064716 -0.022308338 -0.03194340 -0.01037135 0.0661161558 -0.007360627 -0.02923521 0.01141517 0.001497673 -0.01420985 0.03438381 -0.03203514 -0.01804054 -0.01538922 -0.0026678425 0.027398691 -0.04882214 -0.11561188 -0.008509357 -0.01203473 -0.02089645 0.001083068 -0.003061739 -0.11355468 0.027193644 -0.020507654 0.050375480 0.023851383 0.004333629 0.02757450 -0.01461678 -0.01931510 0.006947649
KEGG_FATTY_ACID_METABOLISM 0.19144010 0.177618186 0.19229237 0.18162156 0.195013260 0.17285053 0.18737923 0.2094263692 0.189298006 0.17744684 0.17726086 0.187594417 0.17484769 0.18064373 0.17580318 0.16279037 0.17715535 0.1847771315 0.187298535 0.17615351 0.15131681 0.184344838 0.17544154 0.18540490 0.164558082 0.179209973 0.15666232 0.189591897 0.183358359 0.189661362 0.185937924 0.195641028 0.20399213 0.18301653 0.17977089 0.185912168
KEGG_STEROID_BIOSYNTHESIS 0.29508326 0.295486909 0.26286536 0.27906495 0.291220515 0.28574075 0.30491564 0.3028446031 0.306065643 0.26781522 0.29464863 0.281727962 0.28372727 0.30309918 0.30917324 0.26593252 0.26945212 0.3018824439 0.272449306 0.28920242 0.27852421 0.273019343 0.28299044 0.28594314 0.297497744 0.264419747 0.26785147 0.276188961 0.286487520 0.308034927 0.289095316 0.299848680 0.29269188 0.29943769 0.29468427 0.287313424
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS -0.03581753 -0.092130799 -0.04761225 0.05891582 -0.123502963 -0.08482548 -0.02276997 -0.0448787260 -0.064166255 -0.15073085 -0.07715570 -0.027840150 -0.03137614 -0.08997226 -0.12858747 -0.15452411 -0.15192399 -0.0008490506 -0.141927194 -0.12439918 -0.14957231 -0.052218742 -0.06096819 -0.03648457 -0.146524551 -0.129025468 -0.15339387 0.017340701 0.013213935 0.021006051 -0.008592746 -0.079442545 -0.01531376 -0.09542512 -0.12181560 -0.100962579
KEGG_STEROID_HORMONE_BIOSYNTHESIS -0.00603142 -0.048459074 -0.07974466 -0.01648330 -0.091376743 -0.04645294 -0.05783215 -0.0077100648 -0.032440674 -0.04925962 0.01257962 -0.027085733 -0.05133063 -0.03464357 -0.09107591 -0.04604528 -0.06313163 -0.0037229305 -0.083744196 -0.04403506 -0.07403528 -0.041751578 -0.06718897 -0.06224135 -0.022813686 -0.063619976 -0.05046193 -0.046775240 -0.007732293 -0.031014587 0.038972593 -0.058183774 0.01398730 -0.04158946 -0.10044713 -0.022828144
KEGG_OXIDATIVE_PHOSPHORYLATION 0.23470278 0.265724094 0.26337583 0.24721506 0.255184437 0.25137871 0.25453660 0.2566994039 0.246493165 0.25745496 0.25786805 0.247495875 0.25321032 0.26043249 0.24844391 0.24615206 0.25180784 0.2621473829 0.253121007 0.24466091 0.24444401 0.248324354 0.24596943 0.26085564 0.252493166 0.259461341 0.25704694 0.244689333 0.244937049 0.247126050 0.249275632 0.253150955 0.25606696 0.26126201 0.26134069 0.248688913
KEGG_PURINE_METABOLISM 0.11282696 0.113448858 0.13052367 0.12872555 0.130498773 0.12514834 0.12708974 0.1254518508 0.114374092 0.11746139 0.12720504 0.123909976 0.12501986 0.12926543 0.11864833 0.11039303 0.11837407 0.1306561048 0.120874877 0.11874917 0.12461513 0.118754355 0.11004336 0.12341313 0.111728921 0.125220817 0.12599093 0.120422095 0.116669899 0.120942649 0.125716426 0.120651681 0.12066825 0.12286847 0.11781015 0.119089666
KEGG_PYRIMIDINE_METABOLISM 0.17757771 0.175394817 0.19858724 0.19679890 0.184451412 0.18857531 0.19443581 0.1913521689 0.176616057 0.18757690 0.18742386 0.190866974 0.17707165 0.19343157 0.18609589 0.18058113 0.18517942 0.1962563816 0.174386960 0.18912297 0.18783617 0.175188077 0.17750981 0.19040712 0.177216013 0.198853296 0.18467609 0.173153515 0.179616517 0.173598395 0.177726615 0.185542608 0.19263573 0.19211082 0.17683259 0.184513099
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.10989042 0.093058240 0.09075182 0.09975330 0.110553924 0.08932985 0.10833717 0.1022932484 0.098714538 0.09452201 0.10412503 0.112821342 0.09845573 0.09864529 0.10839464 0.10195788 0.09460140 0.0890330658 0.114926416 0.12373452 0.09891343 0.096051085 0.08806549 0.11101748 0.101678482 0.090367626 0.10014984 0.113927079 0.088757290 0.111944663 0.101911619 0.091610295 0.08631087 0.10449490 0.09680798 0.113666733
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.07589995 0.013164475 0.03073650 0.05497730 0.075187517 0.04629436 0.05684194 0.0721291176 0.091914474 0.05519977 0.08746496 0.050067541 0.05965801 0.06067566 0.08409397 0.10238484 0.01501362 0.0045650662 0.049144983 0.07054669 0.05116744 0.045186268 0.05137738 0.06424885 0.085465393 0.053004029 0.06129235 0.050492310 0.064513199 0.069147728 0.067789023 0.075006091 0.03311465 0.05179666 0.09353812 0.069833588
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.25896290 0.229197097 0.23915083 0.24454874 0.251021905 0.23616587 0.24671301 0.2542987322 0.256828445 0.24146968 0.26145521 0.245522688 0.24379502 0.24900959 0.26862910 0.25530625 0.22947514 0.2349385424 0.237967026 0.24111547 0.26557949 0.234639477 0.23412745 0.23301781 0.258395796 0.215746987 0.23465476 0.256687996 0.239987950 0.250370070 0.237026241 0.252743721 0.22651684 0.23865720 0.25741554 0.244270299
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.18843747 0.186649426 0.17530857 0.15633381 0.178282757 0.18033157 0.18581500 0.1963894497 0.191659866 0.14190172 0.20151595 0.181514394 0.18800238 0.18208434 0.18884446 0.17012565 0.16953990 0.1676338847 0.183699227 0.19745711 0.16337494 0.161194552 0.15788716 0.18351104 0.171161284 0.163754665 0.15047991 0.196948812 0.185610694 0.198192986 0.174172878 0.182779264 0.17802037 0.16062757 0.19890618 0.189941640
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.28568183 0.282786776 0.24961716 0.24491634 0.270528716 0.29605800 0.25836996 0.2521218808 0.281679472 0.24721670 0.32053768 0.274690843 0.28302481 0.30038542 0.30322093 0.29120270 0.28253548 0.2579537498 0.267208046 0.32453395 0.29189041 0.267396603 0.24747811 0.28281020 0.293967599 0.262178623 0.29429367 0.269346291 0.263428379 0.266865452 0.261098171 0.251262879 0.25119395 0.28412517 0.31296991 0.299112229
KEGG_LYSINE_DEGRADATION 0.11363066 0.093971946 0.11756645 0.11921555 0.114150109 0.11417055 0.11382771 0.1282543770 0.110373515 0.10264637 0.10896281 0.119922709 0.11111424 0.09923486 0.10398550 0.09158226 0.11014421 0.0992105519 0.114396655 0.11105307 0.10519398 0.095412052 0.09666140 0.10310679 0.108674463 0.114399506 0.09091906 0.108210445 0.111356587 0.117142092 0.103818204 0.110313192 0.10414576 0.09228489 0.10733176 0.111914878
KEGG_ARGININE_AND_PROLINE_METABOLISM 0.12738384 0.120646580 0.12800721 0.12780121 0.140190182 0.11234716 0.13886310 0.1363147983 0.118339180 0.12495239 0.13387648 0.119717717 0.12674429 0.11413969 0.12760775 0.12051016 0.11112441 0.1060723468 0.135207120 0.11384185 0.11270554 0.120444480 0.10890719 0.13671193 0.148306216 0.127590175 0.12033740 0.129990177 0.120085884 0.143513369 0.139267799 0.139711646 0.12631236 0.12302536 0.13671696 0.129915338
KEGG_HISTIDINE_METABOLISM 0.01037506 -0.009232361 -0.02503732 -0.04007054 -0.004116879 -0.02891744 -0.02515002 0.0005514458 -0.015393247 -0.03216059 -0.03701174 -0.018066447 -0.04417577 -0.03579879 -0.02417860 -0.02971581 -0.02648223 -0.0314952886 0.009196744 -0.04701498 -0.06879069 -0.022838496 -0.03099772 -0.03704899 -0.025519728 -0.039940345 -0.08649494 0.003895911 -0.029842438 -0.000484478 -0.020239498 -0.027308388 -0.01132841 -0.03055363 -0.02153193 -0.036015417
KEGG_TYROSINE_METABOLISM 0.06714488 0.053002829 0.05753161 0.04337986 0.057065867 0.05794194 0.05847814 0.0507298323 0.058615853 0.04701795 0.05759954 0.046542561 0.04954693 0.06556692 0.07181820 0.05370509 0.05763770 0.0690302934 0.044285470 0.04352433 0.06313789 0.067191326 0.04882973 0.05342728 0.052557681 0.041207045 0.04378767 0.064256091 0.055186897 0.048349590 0.069931678 0.042623088 0.06573735 0.06531103 0.05853359 0.057231880
KEGG_PHENYLALANINE_METABOLISM 0.11960304 0.096377593 0.09464200 0.09061793 0.091267769 0.09170094 0.09990226 0.0976280231 0.105007097 0.08739764 0.09597757 0.092011591 0.10469452 0.09925149 0.10437604 0.10710066 0.07942615 0.0989797292 0.119065427 0.09925727 0.10453704 0.086330586 0.09687302 0.10521245 0.097635425 0.085996013 0.09971671 0.107245185 0.084152959 0.091621331 0.102207053 0.107399793 0.10262963 0.09509872 0.08816275 0.098383108
KEGG_TRYPTOPHAN_METABOLISM 0.12707074 0.135904404 0.12002196 0.10198472 0.105456181 0.10258554 0.11263398 0.1471089408 0.134184467 0.09404104 0.12387419 0.114507791 0.10212085 0.12955711 0.09526545 0.11899775 0.10760770 0.1237862285 0.125934177 0.11873044 0.06658891 0.112588368 0.11212948 0.10011186 0.118024833 0.113614802 0.09153418 0.132524487 0.110393708 0.120368868 0.125229509 0.116181945 0.14682099 0.11978502 0.10429972 0.118580441
> pickrellPar <- ssgseaParam(pickrellCountsArgonneCQNcommon_eset,
+ canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> exprs(esrnaseq[seq.int(min(nRowsToPrint, nrow(esrnaseq))),])
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.256075759 0.234440285 0.22365541 0.25164814 0.25617134 0.22440002 0.26825331 0.24363221 0.22303626 0.24453749 0.241659658 0.24784931 0.240912314 0.26440850 0.25175671 0.221994177 0.25951673 0.257749187 0.23737636 0.23373922 0.24102923 0.24394811 0.24421325 0.253552534 0.230189600 0.233117341 0.25308269 0.25087262 2.352772e-01 0.25308477 0.25405537 0.23991583 0.23478740 0.24563546 0.25646515 0.25071702
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.276806659 0.263840724 0.24698443 0.27529933 0.27555689 0.24975236 0.28827170 0.26740093 0.22453250 0.25824366 0.264578233 0.26626941 0.267999750 0.27293682 0.26955574 0.218915231 0.28141656 0.274122454 0.25380024 0.25929889 0.26072040 0.26865139 0.27076349 0.265378539 0.244259988 0.241425821 0.28531051 0.28111746 2.409079e-01 0.26208495 0.26235839 0.27393384 0.25428617 0.26899433 0.27380231 0.26464529
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.308157944 0.298087515 0.29014344 0.31316947 0.31075726 0.29580575 0.33150923 0.30911766 0.27215128 0.29310006 0.318390367 0.31750877 0.303315781 0.32990830 0.31603865 0.276156993 0.32137928 0.328904420 0.28873356 0.28984710 0.29765756 0.29417757 0.30408635 0.309010795 0.284366223 0.286933996 0.32289659 0.31674788 2.939716e-01 0.30287805 0.30290168 0.30124596 0.29981504 0.30880460 0.29585316 0.31112043
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.072900627 0.058114116 0.05095095 0.05552091 0.06878391 0.07768438 0.08213775 0.09250688 0.03556826 0.09156620 0.097878249 0.06956272 0.081520495 0.14591883 0.10114649 0.031874974 0.09204189 0.115726730 0.08879480 0.08133511 0.11303741 0.04597980 0.05930134 0.091652196 0.045442518 0.015179733 0.11243384 0.13618849 5.819542e-02 0.07901269 0.10767281 0.06217197 0.10083457 0.07884946 0.04823275 0.08069438
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.179143833 0.181466412 0.18164218 0.20648051 0.16508263 0.15692126 0.20526979 0.18220460 0.12828973 0.18948921 0.194624757 0.18678502 0.191651374 0.18621396 0.21686165 0.163982758 0.20153270 0.213681011 0.17124101 0.18326784 0.17747109 0.18055651 0.18666452 0.208603904 0.182698854 0.186529878 0.20249678 0.14324407 1.692164e-01 0.17589451 0.20061610 0.16286430 0.16195031 0.19908025 0.18482874 0.20501174
KEGG_GALACTOSE_METABOLISM 0.181131627 0.159926813 0.16270579 0.20573093 0.18044266 0.15543518 0.21952142 0.17843456 0.12359001 0.18349838 0.199111340 0.19452033 0.190574177 0.19551040 0.22253670 0.149654098 0.20567552 0.200581366 0.17030505 0.18223148 0.18954484 0.17613758 0.17006314 0.194920826 0.198422033 0.192448054 0.22245521 0.15408689 1.635711e-01 0.17252060 0.20589447 0.15895753 0.15412635 0.18901486 0.18924635 0.20842567
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.076244940 0.080303827 0.01896975 0.05351930 0.05634166 0.03667802 0.08143338 0.05261833 0.02095408 0.09594147 0.046490176 0.03601321 0.072687156 0.13959149 0.04107588 0.001557203 0.08580840 0.109000508 0.05530623 0.01833645 -0.08023056 0.01932496 0.06300957 0.066003820 0.023771292 0.007102489 0.03086936 0.10270298 -3.157042e-03 0.05314639 0.07495172 0.08280269 0.05626948 0.04257381 0.06298584 0.07433531
KEGG_FATTY_ACID_METABOLISM 0.189817509 0.170872559 0.14155879 0.19190458 0.20061758 0.16220943 0.20719303 0.18088378 0.16687336 0.17684223 0.169286125 0.17914218 0.178915532 0.20998722 0.17201976 0.131109962 0.20936840 0.197325741 0.16514248 0.15827116 0.16387239 0.17860585 0.18319739 0.188238171 0.113651303 0.130750066 0.17770022 0.19465482 1.597647e-01 0.18876629 0.18911247 0.18967056 0.15979790 0.16688397 0.17911784 0.19754478
KEGG_STEROID_BIOSYNTHESIS 0.224283008 0.183502868 0.10641865 0.15431521 0.20673953 0.19381572 0.19919988 0.19375955 0.13759180 0.13279097 0.166353748 0.15479731 0.201859944 0.18441257 0.20240525 0.138935955 0.16161930 0.187730965 0.12780607 0.17277089 0.17211107 0.17687687 0.20523660 0.178291553 0.222139792 0.187421826 0.17910855 0.15862534 1.563029e-01 0.17970860 0.21186843 0.18641454 0.20553433 0.21995063 0.24238713 0.17376305
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 0.007298097 -0.045231480 -0.05615631 0.07155428 -0.03778360 -0.06475813 -0.01631200 -0.01120530 -0.07059793 -0.07173726 -0.040573532 -0.01433368 0.005000649 0.05037597 -0.04733764 -0.070668142 -0.04251391 -0.016724966 -0.03493901 -0.06316513 -0.04576571 -0.03089320 -0.02209954 -0.003440324 -0.082490284 -0.065017438 -0.04750185 -0.03693552 -2.405233e-05 0.03741013 0.04625340 -0.02630856 -0.04838299 -0.05724028 -0.04066866 -0.03635462
KEGG_STEROID_HORMONE_BIOSYNTHESIS -0.046018108 -0.093294319 -0.13746745 -0.05837140 -0.11437771 -0.04362896 -0.07770349 -0.07282807 -0.09993655 -0.05986338 -0.051748220 -0.07057083 -0.081288974 -0.04819890 -0.08749854 -0.080358972 -0.09355664 -0.072350610 -0.13131875 -0.06410751 -0.13561358 -0.09017416 -0.11589119 -0.085631744 -0.094304978 -0.119555451 -0.07166260 -0.03448379 -6.616326e-02 -0.10521967 0.02700273 -0.04856765 -0.05304776 -0.11560595 -0.12890981 -0.06549103
KEGG_OXIDATIVE_PHOSPHORYLATION 0.290044085 0.306375054 0.26041452 0.29564165 0.29454677 0.28682961 0.31516942 0.29225539 0.29624881 0.28190329 0.288965873 0.29838803 0.296122751 0.30714929 0.29408922 0.298005863 0.29592505 0.304180875 0.28081795 0.28727692 0.29838136 0.30109527 0.29148313 0.294331078 0.252378384 0.264546548 0.29654867 0.30641064 3.067693e-01 0.28941630 0.30210492 0.30197862 0.31189519 0.28625608 0.28901836 0.28725201
KEGG_PURINE_METABOLISM 0.121552424 0.114160233 0.11048165 0.13105255 0.11833540 0.10870679 0.12953106 0.12047921 0.08446782 0.11231713 0.112887563 0.11536146 0.105467789 0.13155054 0.12002126 0.113011238 0.12896358 0.123095976 0.11982023 0.10583172 0.10912082 0.11113234 0.10512995 0.109356079 0.099193918 0.103015548 0.12720303 0.13748276 1.143107e-01 0.12051435 0.10972889 0.11378580 0.10276405 0.11768950 0.10730690 0.11186763
KEGG_PYRIMIDINE_METABOLISM 0.159729043 0.145500125 0.14730788 0.17410916 0.15340765 0.14791645 0.16855838 0.15892991 0.11381615 0.15157687 0.147076658 0.15194721 0.127133366 0.17182833 0.15867282 0.142850963 0.16307797 0.161493787 0.14783129 0.14154301 0.14666943 0.14191003 0.14540419 0.146472588 0.114588161 0.131180250 0.16581516 0.18090777 1.515887e-01 0.16056284 0.13622778 0.16268189 0.13979801 0.15559869 0.13630535 0.15387683
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.112712342 0.074567957 0.08695191 0.09240285 0.11298142 0.09506027 0.09739823 0.07764648 0.10950728 0.07593407 0.076879433 0.07931452 0.081605261 0.10786533 0.09769440 0.046974792 0.08948356 0.076841077 0.09165978 0.07828511 0.07203344 0.08737763 0.06590033 0.087495399 0.073193496 0.070563832 0.10778181 0.09237847 6.349400e-02 0.12215027 0.08568016 0.06775927 0.05945302 0.08035606 0.08620309 0.09688249
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.063414089 0.008780948 0.05935336 0.06694159 0.06788012 0.04426421 0.03357666 0.04745672 0.07210759 0.05011682 0.019676287 0.05273708 0.007465601 0.07973086 0.04674425 0.006592034 0.03645575 0.007696429 0.06004590 0.01417259 -0.02089575 0.04782863 0.03721318 0.033513757 0.059026917 0.026399449 0.05354070 -0.01859829 3.487693e-02 0.09841955 0.03620653 0.02255710 -0.01427914 0.03857687 0.09608318 0.07059776
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.234037901 0.189794344 0.20539118 0.22853483 0.22730123 0.19920525 0.19855436 0.22105176 0.21859510 0.21569681 0.192366034 0.19664087 0.202877108 0.24438081 0.22600833 0.162641803 0.19791966 0.190679930 0.19704281 0.18167020 0.20854176 0.21380744 0.20125670 0.201679421 0.212128486 0.203347274 0.19742841 0.19425738 1.833991e-01 0.22861206 0.18710448 0.20444733 0.17838357 0.19817716 0.21897475 0.22036231
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.149779799 0.130868968 0.11141194 0.15213162 0.15707673 0.12253970 0.17713191 0.13281221 0.14628124 0.12815576 0.154689122 0.13889347 0.148455429 0.18582753 0.14490882 0.100438410 0.16119649 0.158609790 0.12845278 0.13377880 0.12834048 0.13474814 0.13427088 0.163849429 0.097733032 0.107920307 0.15085656 0.15995811 1.171796e-01 0.15812798 0.14524879 0.14585176 0.13929386 0.12933917 0.15265580 0.15760441
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.295088488 0.261790244 0.20437749 0.28756505 0.29611186 0.27215510 0.27635622 0.24614956 0.27920993 0.21961975 0.291130821 0.26258549 0.257402155 0.29814324 0.28934456 0.233740001 0.27822280 0.256193143 0.24326695 0.27454545 0.27722539 0.24789039 0.23212598 0.282819863 0.269379426 0.251031182 0.30807137 0.28499798 2.550574e-01 0.27349722 0.26662427 0.24049639 0.27670544 0.24397409 0.28271525 0.28462182
KEGG_LYSINE_DEGRADATION 0.141718140 0.125418015 0.13297959 0.14283107 0.13473057 0.12203529 0.14719941 0.13385750 0.09491781 0.12236495 0.122241586 0.12711931 0.124884910 0.13829366 0.13755243 0.119698191 0.14226579 0.133886134 0.14436915 0.11175177 0.10560139 0.13083694 0.13813000 0.135265809 0.112781050 0.123216658 0.12973261 0.13564156 1.232322e-01 0.13580749 0.12462139 0.13626539 0.10525941 0.13533806 0.13567788 0.14158147
KEGG_ARGININE_AND_PROLINE_METABOLISM 0.135734485 0.123178563 0.10586472 0.12564409 0.14906498 0.11818042 0.14021365 0.12277557 0.09432899 0.11770248 0.140202156 0.10961800 0.124468602 0.13170402 0.12160081 0.090198152 0.12999175 0.127112384 0.11788380 0.11428458 0.11762968 0.13710845 0.11356352 0.130539368 0.104547379 0.117760260 0.12573673 0.11179118 1.059606e-01 0.14634309 0.13320560 0.10643279 0.10948257 0.12483287 0.14500055 0.12996698
KEGG_HISTIDINE_METABOLISM -0.030831971 -0.026347382 -0.05246956 -0.03817025 -0.03711451 -0.05239151 -0.02992710 -0.04339704 -0.04535416 -0.02246956 -0.068943683 -0.05028602 -0.063113563 -0.02707367 -0.05323869 -0.063275978 -0.03173868 -0.039525683 -0.02755053 -0.04591086 -0.06760272 -0.03666616 -0.02528646 -0.040320656 -0.044784334 -0.057674857 -0.06783511 -0.02118087 -4.757559e-02 -0.03079779 -0.03306480 -0.03762207 -0.04374289 -0.03096278 -0.01254511 -0.03899109
KEGG_TYROSINE_METABOLISM 0.017578905 0.013796202 0.01327581 0.04762972 0.01224515 0.03037335 0.04467113 0.03453989 0.01369270 0.03704134 0.022735388 0.02729295 0.010396257 0.04953794 0.03065282 0.024393238 0.04694918 0.040233938 0.01044212 0.02743798 0.03891701 0.04757522 0.02613133 0.039036101 -0.011637129 0.007204219 0.04176325 0.02171444 5.394063e-02 0.02825620 0.04740187 0.02656193 0.05525311 0.01901562 0.06130051 0.03639278
KEGG_PHENYLALANINE_METABOLISM 0.039387037 0.029253986 0.02751646 0.04138092 0.02542332 0.04090945 0.02613385 0.04694566 0.04409473 0.02669409 0.009505697 0.01810860 0.029763207 0.06543376 0.04989771 0.029176209 0.03209528 0.037862444 0.04544696 0.01254836 0.07318278 0.05544060 0.05343313 0.038427201 0.007101842 0.043387306 0.05281127 0.02894583 3.058806e-02 0.04347886 0.06369582 0.02896260 0.02467872 0.04490225 0.06313854 0.01977051
KEGG_TRYPTOPHAN_METABOLISM 0.123296794 0.123012202 0.07613129 0.11525403 0.10856497 0.10334620 0.12704283 0.12708541 0.09159597 0.10202432 0.117859010 0.11469963 0.107325317 0.13152508 0.10459837 0.095553577 0.11230030 0.119066458 0.11008815 0.09174693 0.07821333 0.11181722 0.12158703 0.101828953 0.089254784 0.080564906 0.11224215 0.15882861 9.554444e-02 0.11310320 0.12619907 0.13651820 0.12255016 0.10789454 0.12458913 0.11276116
>
> gbmPar <- ssgseaParam(gbm_eset, brainTxDbSets)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up -0.04270256 -0.1050256 0.12398917 -0.19785894 -0.0706204 -0.08331645 -0.04587976 -0.02691259 0.1493980 0.07636271 0.1292104 -0.02880156 -0.10622416 0.08485902 -0.02108542 -0.10255611 -0.04955077 -0.06055262 -0.1843912 -0.002264514 -0.000616764 -0.08413483 -0.1282847 0.10064219 0.16233229 -0.08391388 0.129510723 0.006051755 -0.0957773 0.05930173 0.07585551 0.122092770 -0.01523058 -0.17022164 -0.02753735 -0.09626334 -0.16239668 -0.1442122 -0.08378182 0.086702046 -0.06829592 -0.01859185 -0.10794134 -0.04824622 -0.02360036 -0.07829131 0.02113254 0.12831408 -0.05187672 0.021500630
astroglia_up -0.24889633 -0.3181389 -0.16250310 -0.34518377 -0.2328486 -0.19025164 -0.20798167 -0.18978759 0.1634546 -0.18567656 -0.1220784 -0.14188750 -0.08219957 -0.18716765 0.08621605 -0.05093007 -0.23268801 -0.28527541 -0.2431186 0.280782610 0.051930564 -0.28603563 -0.2787882 -0.23358730 0.02706818 -0.17339069 0.007161405 -0.128829863 -0.2530055 -0.17991022 0.04954921 0.086976084 -0.19119326 -0.02761475 -0.10601965 -0.21094338 -0.17424458 -0.1764272 -0.25829321 0.183158653 -0.15279730 -0.15292932 -0.25484151 0.12260719 -0.09708606 -0.02624126 -0.03188327 -0.01503725 -0.17238517 -0.105109149
neuronal_up 0.41365516 0.1370905 0.02258175 0.04140498 0.3739370 0.02504198 -0.09469289 0.21037816 0.2898127 0.02594733 0.4223345 -0.22630258 -0.21649319 -0.12661321 0.05458802 -0.15745561 0.22021627 -0.22540274 -0.1018101 0.108388420 0.248267146 0.15400529 0.2284369 -0.03153927 -0.06967695 0.04263526 0.379513854 -0.157687296 -0.1220727 -0.04305240 0.07266218 -0.007533977 0.14634095 0.25658376 0.45865011 -0.07414341 0.08676525 0.2972831 0.20881219 0.005408232 0.28084413 -0.11613621 0.17679797 0.32776928 0.01952200 -0.12391902 -0.24619662 0.49886083 -0.02607648 -0.001236969
oligodendrocytic_up 0.23276809 0.1579273 0.27834655 0.16541114 0.2967757 0.20073958 0.05308861 0.16548555 0.2960602 -0.06212319 0.2511061 0.23363850 0.49638543 0.20198656 0.02902960 0.30191162 -0.09088903 0.17653174 0.2923147 0.173427872 0.233041698 0.12377225 0.2739099 0.17169148 0.36533533 0.30762144 0.395886181 0.210670157 0.3295785 0.20726009 0.20552805 0.352208428 0.23866032 0.36220935 0.33072346 0.38151672 0.10382195 0.2867132 0.40519888 0.104315543 0.27453019 0.08890069 0.02961855 0.35470642 0.42481129 0.14658324 0.13577067 0.21517457 0.09820911 0.073203757
TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up -0.12781345 -0.10424801 -0.003896955 0.23387421 0.25246844 0.3207035 0.1864102 0.2276360 0.264613462 0.16772316 0.1921236 0.150618790 0.2158142 1.480129e-01 0.2547912 0.2467531 0.16111355 0.19983249 0.07535168 0.28372256 0.14028380 0.14573966 -0.04131919 0.09047686 0.1447905 0.10384463 0.174769701 0.15962850 0.23867927 0.147562489 0.17203901 0.32877500 0.12467503 0.2831480 0.21697481 0.2582061 -0.04827454 0.070849773 0.10375364 0.05993822 0.14917783 0.03705593 0.28737667 0.1128391 0.15477895 0.16409778 0.143848674 0.08997557 0.25033466 0.200997387
astroglia_up -0.33567021 -0.09558514 -0.267132320 0.27697125 0.04553025 0.1866003 0.1084145 0.1548024 0.115683387 0.08879166 -0.1794232 0.005649495 -0.1576545 -1.257789e-05 0.0727411 0.1555954 -0.05570396 0.07701213 -0.20774164 -0.04776384 0.13345907 0.02623989 -0.02663276 -0.05953059 -0.1011001 0.02571005 0.182406879 0.02375654 0.06349979 0.063565080 -0.03836509 -0.03293448 -0.03572666 0.1665919 0.16071904 0.2015802 -0.03462372 0.294133704 0.07912455 -0.09833367 -0.01426256 0.25177173 0.13323749 0.2085587 0.11625433 0.09270277 0.061118313 -0.01415236 0.09864426 -0.067173534
neuronal_up 0.07027706 -0.02131532 0.238480842 0.38752317 -0.15659472 0.3577991 0.1892366 0.5672812 0.353841822 0.17010487 0.6047937 0.354282079 0.6087488 1.055863e-01 0.1732358 0.4886717 -0.06147035 0.24909699 0.54129393 0.09127180 0.05607375 0.28403989 0.41755055 -0.07975270 0.5899966 0.33505856 0.102693909 0.28051577 0.08310426 -0.006844963 -0.31495393 0.26595406 -0.30096794 0.4279460 0.10930434 -0.2523735 -0.27065562 -0.331425847 -0.04027485 -0.13510844 -0.02925798 -0.13647458 -0.06576075 -0.1651269 -0.23599409 0.08160665 -0.024158946 -0.39125116 -0.08528125 0.242973089
oligodendrocytic_up 0.26340390 0.20728662 0.238562146 0.03463889 -0.23287645 0.1609936 0.1784241 0.2769686 -0.005855304 0.17838346 0.2103914 0.079351508 0.1988334 1.691518e-01 0.1326108 0.2505812 -0.04892868 -0.03712413 -0.06713938 0.01717354 0.34941440 0.14144163 -0.01200277 0.09049891 0.2205388 -0.16470176 0.007669828 -0.08375967 -0.07398330 -0.023669180 -0.06730557 0.04221507 -0.02535599 -0.1434455 0.04683426 0.1519900 -0.01026107 0.006264224 -0.09514740 -0.09808242 -0.10883555 -0.08778694 -0.07144261 -0.1419069 0.01198113 -0.08184800 -0.006479715 -0.04310793 0.03696027 -0.009964341
TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up 0.23574567 0.27008722 0.11637555 0.16765565 0.1642266 0.03292988 0.2114207 0.13123819 0.2632937 0.255558714 0.12614825 0.22137032 0.16832484 0.2957996 0.2482320 0.20144142 0.29253731 0.3005284 -0.0101724 0.23305725 0.04509015 0.009178942 -0.001041475 0.2798335 0.03802142 0.055982875 0.10438785 0.05182689 0.10224425 0.05216468 0.0862304 0.02155929 -0.003172836 0.06739361 0.06256693 0.26367322 0.11536744 0.01256467 -0.01613898 0.09388852 0.11605589 -0.022074828 0.01870171 0.1159158 0.06165079 0.1766942 0.16406312 0.1409899 0.1558032 0.1268423
astroglia_up 0.08497700 0.03829140 0.30608201 0.15711765 -0.1874617 -0.03283596 0.2290560 0.24698566 0.1847376 0.003580519 0.05081910 -0.04184080 0.23607570 0.1738209 0.1859548 0.11158631 0.02925080 0.2737893 0.3973568 0.25676961 0.39896998 0.362511205 0.397819214 0.3570748 0.25126109 0.160334429 0.40718110 0.34688248 0.36362766 0.26827732 0.3482736 0.31181324 0.269671812 0.31453886 0.29877113 0.44352730 0.40788910 0.14601178 0.31162191 0.29587323 0.37947936 0.349232664 0.33243016 0.2628245 0.34952493 0.2376603 0.14605626 0.3990569 0.3289481 0.2267814
neuronal_up 0.28985543 -0.22610913 -0.06872989 -0.35634904 0.2051659 -0.15883492 -0.1861080 -0.17803520 0.1460343 0.105040208 -0.04944198 -0.33779090 0.29735931 -0.2133380 -0.3174639 -0.16643769 -0.20111679 -0.1413125 -0.1650908 0.01813617 -0.10455488 -0.296484567 -0.187537508 0.2442998 -0.07725316 -0.066574793 0.08146431 -0.06163985 -0.33529820 -0.25395066 0.2275310 0.48981934 -0.150285119 -0.09120100 -0.16014135 -0.01354999 -0.07519059 0.19440942 -0.18040416 -0.21007375 -0.10276626 -0.141371655 -0.21314137 -0.1962376 -0.14976707 -0.1246511 -0.17372631 -0.2207284 -0.1757595 0.1906853
oligodendrocytic_up -0.04365214 -0.01038323 -0.06776547 -0.08472649 -0.1248816 -0.16991651 -0.1094051 -0.06642471 -0.2030105 0.013242268 -0.01680738 -0.03299205 -0.08840665 -0.2023591 -0.0859446 -0.06875004 -0.09073745 0.4037900 -0.0373881 0.12233991 0.07562161 -0.047601068 0.128217901 0.0132698 -0.15651784 0.007475202 -0.04953692 -0.13635011 -0.02535448 -0.07229950 0.1823742 0.37025576 -0.057417938 -0.06801955 -0.05093462 0.09347360 0.14824246 0.18023574 0.43900131 0.01998225 -0.04886937 -0.003561142 0.12171143 0.2173272 0.20198714 -0.2138286 -0.04280936 -0.1078011 0.2334409 0.1350531
TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up -0.01384884 0.1922211 0.1338636 0.11847725 0.1641095 0.006294324 -0.008137892 -0.13724891 0.2054020 0.12997632 0.01119348 0.05979755 0.1010092 0.08196094 0.06026906 -0.000531532 -0.04216870 0.04782013 0.13415875 0.1741715 -0.04346128 -0.02707061 0.0641008
astroglia_up 0.25182230 0.2092300 0.3504668 0.38080141 0.3572364 0.285424310 0.266573973 0.21241946 0.3210299 0.26738072 0.31228683 0.39524758 0.3530827 0.36410787 0.42455013 0.259007098 0.19900055 0.21611551 0.25564425 0.4072161 0.27182445 0.30879011 0.2296599
neuronal_up -0.21981790 -0.1745162 -0.1645862 -0.16331593 -0.1907196 -0.148526527 -0.150903069 -0.20298432 -0.1494018 -0.31979492 -0.07684811 0.12502843 -0.1325836 0.39917847 -0.26476090 0.306810092 -0.03434656 0.11584141 -0.25353924 -0.1629485 -0.11841551 -0.26324244 -0.1689706
oligodendrocytic_up 0.01801927 0.1762533 -0.1216974 -0.02033394 -0.1266508 -0.086965414 0.006808870 -0.05324112 -0.0283358 -0.08040521 -0.01867919 0.07793677 0.1875986 -0.10327650 -0.02771945 0.087825011 -0.13564146 -0.08870616 -0.02615045 -0.0209192 -0.07626177 -0.05744868 0.1065117
>
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> leukPar <- ssgseaParam(leukemia_eset, cgpC2BroadSets,
+ minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
[1] "Calculating ranks..."
[1] "Calculating absolute values from ranks..."
[1] "Normalizing..."
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP -0.11212188 -0.09106815 -0.121150864 -0.08143375 -0.088090518 -0.07340947 -0.10376635 -0.12329046 -0.107490316 -0.1094321479 -0.09602253 -0.097841141 -0.052252012 -0.107114347 -0.10907601 -0.07366425 -0.12469120 -0.105311438 -0.11210642 -0.07831097 -0.095506069 -0.09272797 -0.080016602 -0.0601701101 -0.086388455 -0.086143328 -0.07964313 -0.07476053 -0.11573733 -0.106800817 -0.07058489 -0.083557328 -0.08462769 -0.090099523 -0.0549047537 -0.104821669 -0.12270687
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP 0.12773870 0.11958013 0.169039831 0.08039046 0.079764086 0.04745847 0.17432542 0.10197508 0.108268340 0.2006370201 0.12760627 0.136610607 0.094614756 0.075754012 0.13272714 0.10349286 0.08997838 0.105152129 0.07972599 0.04842713 0.156201488 0.10861902 0.048660863 0.0486013305 0.094428151 0.067025764 0.07166594 0.02581748 0.01906544 0.053825100 0.11114079 0.146989381 0.08036877 0.070876416 0.1065750807 0.032006331 0.03126135
WINTER_HYPOXIA_UP 0.19660336 0.22220588 0.208150808 0.20369715 0.194220520 0.18637683 0.18791267 0.18394723 0.191934075 0.2073623135 0.18961007 0.206889571 0.227895816 0.218581670 0.19144735 0.22310948 0.19439608 0.202960622 0.20949776 0.19542339 0.216907511 0.24031950 0.208217532 0.2011029977 0.234533054 0.221475821 0.19919427 0.23800347 0.20715801 0.230102555 0.24544630 0.211888487 0.22075250 0.213354811 0.2209719414 0.212552165 0.19720964
PYEON_HPV_POSITIVE_TUMORS_UP 0.12936217 0.08608186 0.156095439 0.04512521 0.100883198 0.11208812 0.12352973 0.17187068 0.153348975 0.1703012802 0.11051421 0.170675622 0.015252592 0.094679684 0.14160524 0.08032573 0.13750853 0.138672606 0.08985131 0.03661538 0.105799747 0.08113882 0.107166119 0.0506252281 0.047816290 0.095272447 0.10133515 0.08434566 0.11544536 0.046634453 0.06811758 0.136585794 0.09329885 0.066439827 0.0424873211 0.055346301 0.11044267
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP 0.10497861 0.11810250 0.130550079 0.08824334 0.067996562 0.09001761 0.10880848 0.09112328 0.114928671 0.1341928379 0.11162537 0.121156220 0.097889549 0.134823238 0.11398214 0.10943782 0.10538109 0.110901558 0.10004585 0.07652972 0.124448823 0.09605908 0.095401105 0.0800272992 0.125435027 0.107655114 0.07785774 0.11689738 0.10900193 0.126404590 0.13500916 0.118357443 0.12482627 0.132783820 0.0875660360 0.100749901 0.08896426
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP -0.14415962 -0.13112123 -0.148059446 -0.13794539 -0.137336129 -0.12385178 -0.12980927 -0.14141721 -0.145591804 -0.1413958552 -0.11800610 -0.144207294 -0.131972015 -0.141042585 -0.12498393 -0.14357730 -0.12949535 -0.154721081 -0.14240748 -0.12956549 -0.143591188 -0.13236731 -0.149298176 -0.1300145478 -0.131174376 -0.136769869 -0.12031729 -0.13417144 -0.14801656 -0.103740991 -0.11897875 -0.131464086 -0.12259302 -0.128755678 -0.1259053782 -0.135984581 -0.13075821
LU_TUMOR_VASCULATURE_UP -0.08611663 -0.03840696 -0.075208780 -0.06571226 -0.059283399 -0.09743345 -0.01241906 -0.11715637 -0.095094587 -0.0942931758 -0.04907607 -0.091230456 -0.074117889 -0.052525843 -0.06551791 -0.04611678 -0.06288770 -0.095388286 -0.05466379 -0.02196421 -0.089002940 -0.02903084 -0.099934618 -0.0328273529 -0.059930837 -0.093726300 -0.06905892 0.03385055 -0.10159676 0.062777131 -0.04579346 -0.064021288 -0.02096713 0.041382070 -0.0659072134 0.004541717 -0.08085065
KORKOLA_EMBRYONAL_CARCINOMA_UP 0.14802750 0.19989559 0.193531409 0.19043055 0.164415884 0.14670572 0.13835951 0.15782717 0.158620695 0.1923823767 0.17142120 0.191193516 0.189426831 0.200421860 0.17161690 0.21494495 0.18205192 0.192282258 0.16595727 0.17568860 0.212460788 0.19870684 0.195131434 0.1589439546 0.191376696 0.173976522 0.15799413 0.19036604 0.19127428 0.176196755 0.18543632 0.176852454 0.19522737 0.136840003 0.1714436876 0.171497790 0.18616571
KORKOLA_TERATOMA_UP 0.22823416 0.29024180 0.231155370 0.23171935 0.254748989 0.19408563 0.16835792 0.16188829 0.112118254 0.1565428797 0.20383020 0.123476972 0.217612011 0.244082034 0.22362179 0.28040203 0.20831738 0.168287700 0.24110595 0.23418356 0.244983055 0.25692773 0.200311939 0.2184469742 0.248702703 0.190689786 0.21178104 0.22717410 0.21281765 0.198438514 0.21014560 0.161257116 0.19694428 0.158841418 0.2076681127 0.196667083 0.21540144
KORKOLA_YOLK_SAC_TUMOR_UP 0.34466298 0.39892106 0.377886303 0.33108088 0.355059703 0.34014296 0.33424236 0.33551668 0.322514107 0.3587143377 0.35616777 0.345656031 0.361905734 0.356409761 0.34356338 0.36466181 0.35676080 0.353135417 0.34782607 0.35557146 0.369519925 0.37855110 0.340752613 0.3310743436 0.310692783 0.333271917 0.33092650 0.35381284 0.34636036 0.330627105 0.35041188 0.339198683 0.36176745 0.298834876 0.3344121129 0.355416500 0.34180114
KORKOLA_CHORIOCARCINOMA_UP 0.44015614 0.48855227 0.450504964 0.46641488 0.448745786 0.41967427 0.40468719 0.44145971 0.455353414 0.5056625648 0.49198361 0.489745578 0.490534332 0.483410654 0.48684370 0.50623699 0.50398811 0.496025889 0.46027781 0.48204686 0.502594106 0.49342943 0.461528278 0.4453763188 0.453555580 0.457458981 0.44222231 0.48845097 0.47883248 0.485213780 0.48703015 0.459726900 0.46124201 0.434116406 0.4887206089 0.467923068 0.49059426
KORKOLA_SEMINOMA_UP 0.13847750 0.17850772 0.174597045 0.16508981 0.157223586 0.15596102 0.14187743 0.14411233 0.155857399 0.1758869779 0.17913681 0.168367099 0.161656280 0.177625715 0.15933775 0.16766991 0.17459358 0.187638049 0.16053712 0.18068610 0.160177064 0.16297719 0.143814313 0.1368714657 0.146708281 0.137036347 0.13672037 0.16405538 0.15687579 0.149515564 0.15499412 0.151293558 0.16531883 0.125764891 0.1551887231 0.172244543 0.16315928
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP 0.27744218 0.26350935 0.297888085 0.25976966 0.276608184 0.25693663 0.27761830 0.28848813 0.286664487 0.2762852086 0.27840239 0.291426599 0.282808179 0.294631962 0.29385340 0.26740892 0.28461746 0.296478631 0.29646299 0.26712951 0.297136943 0.29037251 0.290182379 0.2766321689 0.294832624 0.290120635 0.28546834 0.29985442 0.31836713 0.295872223 0.25619716 0.283982155 0.29792700 0.299964305 0.2675484590 0.301101215 0.29995819
HOLLMAN_APOPTOSIS_VIA_CD40_UP 0.20838568 0.20620590 0.226021285 0.18903855 0.205996318 0.21204142 0.21967797 0.21308316 0.201127727 0.2021400473 0.20717155 0.215017814 0.187117852 0.219969815 0.21173231 0.19604622 0.21329915 0.212552604 0.19626079 0.19827681 0.211735913 0.19112536 0.203069987 0.2197126547 0.197947624 0.204388551 0.19946042 0.20608121 0.21291368 0.212708378 0.19862400 0.209122222 0.19925121 0.211899137 0.1938569725 0.222442050 0.21241407
LIU_PROSTATE_CANCER_UP 0.12333806 0.12822475 0.122836081 0.12725808 0.140594244 0.12825347 0.11034224 0.11649062 0.120184024 0.1301693730 0.12229130 0.129704667 0.137069254 0.111577549 0.11871748 0.11882426 0.12222041 0.139520829 0.11722272 0.12381120 0.128360065 0.13208683 0.142162149 0.1356536483 0.114693190 0.133318936 0.13748781 0.12832984 0.11667838 0.122081679 0.13437113 0.135333521 0.14198109 0.117064049 0.1415429031 0.128631348 0.11727950
LIU_SOX4_TARGETS_UP 0.08191204 0.05214134 0.096757396 0.07523797 0.079421912 0.07708861 0.08083627 0.10566201 0.079132766 0.0800895023 0.09502955 0.065630075 0.033165065 0.070986201 0.10605029 0.08258342 0.08768873 0.071996983 0.11390213 0.09018520 0.065872711 0.02685959 0.066144677 0.0727056296 0.082403808 0.073595763 0.06589577 0.06643292 0.09747230 0.106162263 0.04897972 0.066492306 0.06313290 0.112840981 0.0424372639 0.065643621 0.10517315
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP 0.12962537 0.11610080 0.145466087 0.12133965 0.151001465 0.12542172 0.12193757 0.11684710 0.124876198 0.1227735670 0.12962045 0.133337998 0.145216907 0.141828051 0.15001820 0.13815100 0.13460255 0.151878290 0.13727416 0.15746327 0.139912030 0.13476324 0.129655986 0.1284177003 0.132525587 0.130459851 0.12869022 0.13923393 0.13259415 0.155502893 0.13899383 0.126465783 0.14275177 0.146336368 0.1220863251 0.171552323 0.12417440
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP -0.04699784 -0.03856334 -0.028301448 -0.03891271 -0.045089149 -0.03704312 -0.02630941 -0.02816459 -0.029559739 -0.0534978383 -0.01366122 -0.041830107 -0.050639545 -0.040411674 -0.02102565 -0.03970615 -0.01799213 -0.033341689 -0.01897268 -0.01365414 -0.028107224 -0.02713442 -0.046683538 -0.0206629560 -0.018977519 -0.038659175 -0.03223894 -0.01494866 -0.02004138 0.028290459 -0.02212699 -0.038100635 -0.02119184 0.003239358 -0.0369081395 0.014342415 -0.01112552
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP -0.09394028 -0.10883789 -0.125696986 -0.07648813 -0.114219799 -0.09129576 -0.10820034 -0.09787250 -0.092631165 -0.0637997483 -0.07766220 -0.094268793 -0.082937625 -0.106384923 -0.08192685 -0.10758882 -0.08542658 -0.092203040 -0.06488157 -0.09003358 -0.111067169 -0.08970828 -0.114620536 -0.0850125408 -0.059028109 -0.122409700 -0.11287838 -0.08916244 -0.09472273 -0.077911670 -0.09390619 -0.097644568 -0.11001932 -0.078106059 -0.0940344476 -0.091955745 -0.07766899
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP 0.02510931 0.08834848 0.080971697 0.01114658 0.025264412 0.04515388 0.06017182 0.06139166 -0.001637575 0.0902450722 0.02735733 -0.004243082 0.008884452 0.024612352 0.02882780 0.04029161 0.10199346 -0.025891095 0.01797175 0.03194774 0.099164270 0.07272077 0.001372288 0.0386279383 0.018516022 -0.003201053 0.04261062 0.04512323 0.05409370 0.082268487 -0.01156691 0.038932474 0.05063402 0.046801355 0.0762341100 0.031483923 0.09146968
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP -0.01159980 0.01773789 0.002741870 0.01471238 -0.003972485 0.01295277 0.02605081 0.02748918 0.012317275 0.0001521724 0.01504880 0.002445162 0.026606924 0.001673537 0.04936615 -0.01373036 0.01157459 -0.001213928 0.02950728 0.02709116 -0.001369139 0.01070392 -0.008326614 0.0005865785 -0.006947417 0.003683486 0.01476815 0.00833425 -0.02602648 0.005669794 0.02372157 -0.002592865 -0.01080445 0.018411711 -0.0002326556 -0.019837822 -0.02111218
FRASOR_TAMOXIFEN_RESPONSE_UP 0.06343555 0.06524186 0.076096149 0.08623646 0.035901095 0.05553414 0.04813651 0.05000595 0.018630799 0.0361654200 0.04294741 0.045994056 0.084165291 0.039521918 0.04147761 0.03215540 0.04010818 0.043314016 0.07676386 0.04559031 0.070087913 0.07091543 0.059398083 0.0706534110 0.071532990 0.068066629 0.06426931 0.07338332 0.08518933 0.065149663 0.07183749 0.066367920 0.06594029 0.077125008 0.0927989288 0.074142612 0.07559066
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP 0.03004809 0.05432805 0.001432391 0.02459771 0.011252625 0.04038848 0.02972862 0.01314790 0.002092703 -0.0156113936 0.04748579 -0.011117702 0.009640799 0.033918561 0.03840938 0.04608757 0.01172223 -0.005214653 0.03919416 0.04798752 -0.003693506 0.02843361 0.014212574 0.0239450749 0.022041404 0.002291239 0.03366971 0.04054535 0.02752102 0.053112241 0.05954476 0.008942285 0.01327435 0.032914846 0.0378134578 0.024061336 0.01399793
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP -0.03953071 -0.05465739 -0.007602480 -0.09969782 -0.064649394 -0.07536982 -0.04164320 -0.05312600 -0.043319892 -0.0119909722 -0.05473042 -0.040898014 -0.087901954 -0.049785859 -0.01812754 -0.08046669 -0.04513855 -0.042191116 -0.06131214 -0.08200335 -0.042998833 -0.05742151 -0.078783092 -0.1056325522 -0.069303843 -0.057059264 -0.07539755 -0.06329446 -0.06679513 -0.049903218 -0.05732776 -0.036949074 -0.04247288 -0.046862641 -0.1023930938 -0.071387634 -0.08894461
WATANABE_COLON_CANCER_MSI_VS_MSS_UP 0.04819844 0.08558284 0.055708783 0.10324646 0.050709634 0.04995449 0.04822270 0.03763487 0.066913831 0.0260843037 0.03852020 0.041160906 0.092662161 0.050620558 0.03429650 0.05177460 0.08589703 0.046940975 0.04818196 0.04030422 0.077704576 0.10913606 0.057248585 0.0744440801 0.078206610 0.092934179 0.05650890 0.06626172 0.06222949 0.035216390 0.08404366 0.042016648 0.04474503 0.077050552 0.0877448713 0.057929757 0.02811160
>
GSVA.Rcheck/tests/test_zscore_newapi.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> ## 2023-11-10 axel: simple test script for method z-scores, new API
>
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db
> library(GSVA)
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 1.4171739 -1.3444519 -0.99052898 0.4203395 1.30716224
g2 -0.7281951 0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754 0.09779699 -0.6792548 -0.09124045
g4 1.0735382 1.3156255 0.15588330 -1.8079608 0.48531108
g5 0.7229884 -0.9162342 1.93982245 0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> zscorePar <- zscoreParam(X, gs)
> zscore.es <- gsva(zscorePar, verbose=FALSE)
> dim(zscore.es)
[1] 100 30
> zscore.es[seq.int(min(nRowsToPrint, nrow(zscore.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 -0.397989121 0.63767552 -0.71152962 0.95681431 -0.39154705 -1.0418650 0.76943162 -0.22652269 -0.03794476 1.23795689 0.54741085 0.541307906 -1.3025217 -0.07350935 0.5617042 -0.110558260 -1.48434203 0.48341124 1.4582348818 -0.6596565 0.42366570 -1.18733982 -1.38666349 1.77213207 0.49521884 -0.54625805 -0.46923643 -0.326809131 2.03448230 -1.565153279
gs2 -0.292150055 1.00652251 0.59082177 0.60360826 0.09399124 0.3990216 1.16059005 -0.51857868 1.57864006 -1.82507931 0.27951753 0.015075493 0.7420740 -0.26993044 -0.1951051 -1.228360534 -0.29127936 -0.38907836 1.7217817461 0.4289776 -1.05871842 -1.92619800 0.16799779 0.27006041 -0.01617003 0.22027905 1.62510577 -0.140877183 -1.58374028 -1.168799069
gs3 0.286561399 -1.05214008 0.44954052 0.05225134 -0.27816203 0.5745265 -0.08816684 0.55254769 -1.29875323 1.56194900 -0.05237899 0.263111063 0.9526169 -1.98894869 1.9629224 -0.260586823 0.03510070 0.11049165 -1.0053564642 -0.7887344 -2.62545010 0.37942785 -0.80210329 0.63432226 1.52546755 0.14200823 -0.95287090 1.269227032 -0.32940645 0.770986212
gs4 -0.354767925 0.21855737 -0.54770518 0.57023369 -0.40119719 1.1654367 -0.85027787 0.05797497 -0.57666632 -0.19441172 -0.84753296 -0.201717192 -0.4443591 0.31037957 1.4397151 0.144981987 1.28913756 -0.76109926 -0.8188041253 -1.1193965 -0.34735329 0.02731708 0.47050049 0.36107874 -0.24978630 0.69621376 -0.34730205 0.335664905 -0.50390439 1.479089488
gs5 1.053567012 -0.90096227 -1.22439233 1.38286556 0.72832395 0.2446611 0.64214154 1.67034063 0.94014544 -0.56337436 0.13297430 -0.003270595 -0.4892865 1.04965180 -0.9017189 -1.422587378 0.25687151 0.34246303 -1.3100855881 -0.4117660 -0.56998370 -1.04747710 -0.59951317 0.38286581 -0.42463836 0.29869964 0.69420619 -0.224502898 0.01378260 0.259999076
gs6 -2.244409734 0.99135128 -1.25755227 -0.48107465 0.77088243 1.1587775 0.84165607 0.70800821 0.04455796 1.20866884 -0.08722013 -0.339734762 -0.3068380 -1.26475846 0.1691293 -0.016173483 0.08935879 1.04034445 -0.7302067427 0.3619944 0.09955336 -1.47161635 1.46668998 -0.57430525 -0.57827541 1.08697889 -0.36812846 -0.225673601 -0.63259981 0.540615686
gs7 0.052740026 1.67321048 1.06844511 -0.63335768 -1.29665110 -0.1715307 -1.66933194 -1.66163147 0.96745704 -1.98236849 0.39924531 0.780997272 1.5031445 0.82365265 0.7355819 -1.291690222 0.59198917 0.44201538 0.7748958150 -0.8715253 -0.42109173 0.38678646 0.62509742 -0.34088470 -0.73371942 0.45694938 -0.16347393 0.245014602 0.54802183 -0.837987628
gs8 0.128940466 -0.29023472 0.89066527 -0.61440040 -0.38274282 0.3546077 0.27907069 0.36742752 -0.96538900 -0.68424061 0.41316821 0.891427943 0.8562297 -0.82606670 0.9954917 1.271105299 -1.57441049 0.58613131 0.9237786732 -0.5526007 -1.00447106 -1.18216783 0.80591481 0.04182974 1.50238637 -2.48809418 0.67198869 0.329970369 -0.23288683 -0.512429049
gs9 -0.529924217 -0.50455633 0.14056762 0.82608534 -1.08452996 -2.4214825 -0.82702123 -1.51917889 -0.46117537 0.51536039 0.59351509 -0.477518222 -0.9141765 -0.36202472 0.2121035 -0.573687565 1.07691896 1.45448291 0.9987170368 -0.3781715 0.53631214 -0.44654865 1.24408983 0.30795693 -0.37080302 1.21990637 -0.38428269 -0.709115714 2.34614281 0.492038227
gs10 0.818321331 -1.51317539 -0.69457073 -0.49203352 0.36057893 -0.2397877 1.75081101 -0.06994105 -0.63367045 1.19094149 -0.90730458 0.767877575 -0.7928538 -0.06625141 1.5861559 0.979933067 -0.44783025 1.27989685 -0.4868701103 -1.0117896 0.94361547 1.85673623 -1.61731898 1.21625436 -0.28647246 -2.18059795 0.27744213 -1.003408010 0.30192017 -0.886608508
gs11 0.367678555 0.91252056 -0.42227266 -0.97087272 1.79158580 1.2585482 0.94342732 0.33332996 0.25752326 1.08956985 0.42462020 -0.463361537 -1.0340709 -0.62851508 -1.0342834 -1.514469249 -1.59087446 -0.08592467 0.5711694824 -0.2126554 -0.78142230 -0.16484959 -0.11708371 -0.06365675 -0.30699322 -1.78437695 -0.38348966 2.096264437 1.38197003 0.130964576
gs12 0.407633162 0.06089458 -0.03551973 -0.80557241 0.28472856 0.3839476 0.03138942 0.13026214 1.25696925 0.64914081 1.03413817 -2.014871071 -0.6371566 -1.64623803 -0.4174678 -1.889613999 0.17910813 0.02329786 -0.0009531196 1.3544298 0.64070445 -0.12299599 0.34538224 -0.04683912 0.06609172 -0.03387139 1.19121339 0.002288050 -0.67084599 0.280325902
gs13 1.117333034 1.17636696 0.90610556 -0.20339948 -1.76940395 0.6695672 1.67072725 -0.88508357 0.21042968 1.10554677 -1.20938609 -0.936796828 -0.5420542 -1.95749072 -0.1021446 -0.326335251 -1.38725541 0.03867057 1.2922253522 -0.2178358 1.11848269 0.61807105 -0.58824635 0.51758303 1.16189807 -0.11542606 0.56125057 -1.102475834 0.07801156 -0.898935092
gs14 -0.087991419 -1.48961560 -1.81093995 1.52077150 0.42263796 -0.2523003 1.81177614 -0.98653014 -0.44359835 -0.78718957 -0.27032118 0.208913565 1.4209980 1.20266088 1.0754392 -0.017917459 -0.55564302 0.04818988 -0.0639771402 0.5514408 0.12200747 -0.61335181 -2.18595402 -0.10832614 1.30303553 -0.18875480 -0.15271362 -0.366281115 -0.10674437 0.800279063
gs15 1.343950151 0.42076882 1.38439882 -0.88759686 -0.91178620 -0.4662795 -1.04143070 0.63814001 0.82957344 -0.29962403 -0.07941374 1.630590421 -0.5871337 -0.07434265 -1.5095501 1.553793983 -0.34571793 -0.82240473 -0.0947857521 0.8003060 0.21116056 0.32367880 0.86106297 1.65628788 0.97789380 -1.11080368 -1.05693195 -1.075624856 -2.14302463 -0.125154750
gs16 -2.280647404 1.45443048 -1.15615266 1.22715648 -0.91887150 -0.8774493 0.59718755 -0.53354106 -0.56650374 -0.69692215 -1.94787175 -0.263432001 1.8506749 -0.38045289 1.5196647 -0.171439192 0.23374260 0.12207975 -0.3457662199 0.8058231 -0.04857341 0.06274313 0.24285089 -0.52530011 0.36494819 0.51658411 -0.01130771 -0.356448130 1.77208671 0.310706625
gs17 -1.793915600 -0.76504524 0.63042343 0.52009464 -0.76953891 -0.6130846 2.30516686 0.87030325 1.22942353 -0.38676648 0.28786780 -1.294578572 1.0048342 0.34124188 0.6789841 -0.427903451 -0.26781132 0.36824855 0.1448156182 0.2312562 -1.65929393 1.39937404 0.85491251 -0.82632158 -1.70289841 0.74965589 -0.12891045 -0.156350687 -0.69636392 -0.127819267
gs18 1.076598555 0.66297942 0.31193924 1.21825571 -0.97634484 0.2376817 0.95228421 -0.69548369 0.64407889 -1.54705843 0.78530509 -1.141744986 1.0737459 0.20826231 -0.7801733 0.779895003 1.28313586 -0.72108935 -0.2461143875 -0.7458027 -0.38409736 -0.53680945 0.39463325 0.46243990 -0.97160166 -0.73933254 0.11490689 -0.850845941 -1.31226102 1.442617701
gs19 -0.932647493 0.36466764 -0.35976335 -0.48336730 -1.40727655 -1.7654296 -0.20079225 0.78943776 1.05075289 1.00527802 -0.38819134 0.067221765 -0.3143035 -0.09898034 -0.3791052 0.742819045 1.03125690 -0.29435736 -0.8584556405 1.5373474 -0.10243970 -0.45157605 -1.14712245 -0.58329174 0.09597807 0.98132256 0.98914383 -0.803965353 1.03267715 0.883162283
gs20 -2.507512451 -0.09179266 0.89256971 0.73127951 1.29936004 1.0227561 1.19748908 -1.12254621 0.39765236 -0.32497812 0.92840593 0.535525595 -0.6698568 -0.67309618 -2.7854267 1.470107881 -0.08598559 1.74783328 0.5261305573 0.1206040 0.50408329 0.08501165 0.83770748 0.10297851 -1.04236424 -1.27093846 -0.79581565 -0.156645031 -0.34413218 -0.528404617
gs21 1.590666101 1.21727966 -0.51796988 -0.70384659 0.47869886 0.6412920 1.08855268 -0.47402976 0.08376531 0.13287875 -0.58417864 -1.418465566 0.3586347 -0.06298446 1.0527743 -2.146897926 -0.23073419 -1.51825713 -0.0886423308 -0.8228190 -0.89776066 -0.01018669 0.03607537 -0.23848721 -0.91307940 2.16316601 0.88039149 -0.180082700 0.42559671 0.658650146
gs22 -1.314146576 0.56105707 -0.29581903 0.01879511 0.70153285 -0.4595619 0.79526977 -0.30610624 -1.59054925 -0.12272649 1.47363794 -0.919840374 0.3988845 0.50906124 -0.1078853 0.005275414 -0.80093636 0.02875750 0.1796627484 0.8606802 -0.14613823 -0.08254134 1.34492879 1.33240524 -0.72078684 -0.13081350 -1.79095355 1.829439862 -1.03960553 -0.210977661
gs23 0.007467771 0.87566015 0.10324376 0.43422509 0.89948175 1.4248760 -0.42838198 -0.63377944 -1.60531538 -0.81617333 0.71976579 0.178541229 -1.5026766 1.31351070 0.5908263 0.295870288 0.31272798 0.41614095 1.5239090790 -1.0149427 0.50905084 0.08055801 -2.05892070 -1.43447026 0.75255573 1.23995792 -0.53070949 -0.671543192 -0.97238791 -0.009068384
gs24 0.962632242 0.95541708 -0.19066384 -0.23175174 -0.76110030 -1.4063679 -0.89610030 0.66372973 -0.80965792 0.08779694 1.43555471 -0.290334626 0.2202661 -0.20314804 -1.7974438 1.986615879 0.30858557 -0.81071709 -2.1361827974 0.5564193 1.76375887 -1.03057351 1.32045107 -0.52316315 0.55080127 0.67747310 -0.41157504 -0.004477188 -0.66154101 0.675296303
gs25 0.750300473 -0.69054276 1.18919625 0.22555676 -0.89812453 -1.9043047 -0.08872006 -0.53073008 -0.25382802 0.61889062 0.54487413 0.150650635 -1.1560727 0.67452679 -0.4169377 0.301273856 0.27364471 2.12016724 0.2984327507 -0.7254619 1.57708274 -2.55299380 2.35308624 0.03326361 -1.15647532 -0.70205328 1.05030170 0.062511954 0.46103929 -1.608554943
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+ grep("^REACTOME", names(c2BroadSets)),
+ grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- zscoreParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+ minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.08200762 -3.52041732 -3.26174022 0.51755585 4.3317957 0.20731183 0.79679064 0.79926124 0.8990293 -0.3162241 1.37146559 1.28865093 0.08780809 -0.04487147 -0.91082622 -2.01743735 -3.12498579 -2.43416998 1.66792540 0.63671241 0.98429879 -2.77176425 -2.57368171 1.08251788 1.86537795 -0.2611243 0.3413125 -0.86055908 -1.49156413 1.32126944 2.69602243 1.710794035 0.8409827 -1.34346099 1.04123139 0.362705265
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.22642469 2.71693263 -0.10717960 -2.55590909 1.8299224 -0.47957924 -0.54472874 -0.02445334 0.9176705 -2.7381498 2.48189970 0.83060592 0.38079534 3.38221199 -0.32877740 -2.83603934 -4.22277480 0.30241154 1.04250419 1.46120065 -2.03473559 -1.21891964 1.08436248 1.06426425 -1.55401694 -0.5226624 -1.2189195 -0.45981366 -1.44418236 -0.97635055 0.50837155 0.687584202 2.5479218 0.26221667 2.58838008 -1.048488516
KEGG_PENTOSE_PHOSPHATE_PATHWAY 1.36770713 -2.36222774 0.04423311 0.12728501 4.5866555 0.73826068 -0.30430005 1.12280301 0.7386334 -0.4741849 1.94803182 0.77746818 -0.21649571 1.53618820 -1.14034304 -2.06467802 -3.35703927 -0.52856032 1.23074711 -0.38012652 1.09162981 -1.97458243 -1.97155134 0.40676902 -0.11013586 -0.8840621 -0.1723332 -0.55469059 -1.82128559 -0.27395469 0.21881375 1.100739928 0.2091012 -0.73264959 1.63276978 0.445364274
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.24894806 1.15822465 -0.63403859 -2.85893527 -0.1383472 -0.23236162 -0.85909142 0.52113731 0.4042918 -1.2811704 1.65377601 1.05051126 -1.44312727 1.72029902 0.59548843 -1.29956124 0.13453374 1.14525277 1.29207698 0.58036810 0.53523531 -0.44979114 -0.57051676 -0.15789451 -0.25900848 -2.1421868 0.4292179 1.66346748 -0.71371117 -0.01810125 0.12724512 -0.774738588 0.2843053 -0.03222607 0.34212600 -0.021697443
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.09155076 -1.97525177 -1.45276746 -0.07481523 3.5602457 0.21410187 -0.46891224 0.48276577 0.8301800 0.2782034 1.76137958 -0.30167366 -0.36866461 1.40519024 -0.46806431 -1.89929335 -2.77414056 -1.44200425 0.06351456 0.43244830 0.47487440 -0.05968271 -2.47979046 0.88521908 1.45849373 1.4370859 0.7227373 -2.42689891 -2.32001921 -0.69902703 1.80940353 1.445144270 1.1884455 0.36808537 0.73860677 -0.436670241
KEGG_GALACTOSE_METABOLISM -1.50220635 -2.12210786 -2.26086463 0.19222532 3.7806514 -0.02135668 -0.06191917 0.04740533 0.3036345 0.8632324 0.86542561 0.79337892 0.94383717 0.64846184 -1.52736862 -2.10108047 -2.57431539 -2.81169968 1.46044938 1.54579783 2.08963590 -1.37567056 -3.06980601 1.26834691 2.35203893 -1.1214375 2.0145262 -0.70745876 -3.08391089 -0.38893891 1.12194963 1.625915928 -0.1365118 -0.66174770 1.84065605 1.770831772
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 1.62312696 -0.15873213 0.21618956 0.46858637 0.9166095 -1.04599221 -0.27045669 1.11594251 -0.7483182 -0.1238161 -0.08764850 -0.32826008 0.34447096 1.24438098 0.61296527 0.15432850 0.45526120 -0.36519590 0.20463352 0.04105416 -3.40788046 -0.10615080 0.03162673 0.30778305 0.76679284 0.7047822 -2.6927801 -0.49668598 -0.74070175 -0.19230287 0.78253260 0.019056184 1.1861060 0.56044201 -0.99809984 0.006350524
KEGG_FATTY_ACID_METABOLISM 1.35637843 1.25200293 1.07298339 -1.71740038 2.3901222 -0.36157315 -0.61828083 2.30667544 1.7661146 -1.3820937 1.13392622 0.56871041 -0.79388010 1.09003603 -0.36094837 -2.90971040 -1.94439447 -0.01160654 1.33989630 0.15215352 -2.89938246 0.22556399 -0.77232732 0.57215286 -1.83412952 -0.7752354 -4.1289987 0.02530249 -0.63474809 -0.08583303 1.30223207 0.651511781 4.0322588 0.16603308 0.29172425 -0.465236301
KEGG_STEROID_BIOSYNTHESIS 1.36553599 -0.12013577 -3.08293491 -1.34327805 1.3358376 -1.11364214 1.86689706 1.85283136 1.5670901 -1.7482283 0.54388973 0.03810215 -1.44328919 1.85735478 2.10172330 -2.62881691 -2.32801957 1.24532010 -1.02033468 0.69913015 -0.29822576 -1.97008651 -0.19118335 0.33269001 1.52165526 -2.1837464 -2.2547570 -1.83792686 0.06447423 2.18187799 0.88568269 1.120120992 1.0123686 1.94734636 0.53060126 -0.505924347
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS -0.08350356 0.59893449 -0.18051314 1.46849025 -0.5398104 -0.94926659 1.14314746 0.90284639 -0.9560743 -1.7658533 -0.74679073 0.45581317 -0.76088516 0.75908154 -0.92291196 -0.68856752 -1.36785514 0.55938543 -1.85379029 0.65684292 -1.41481016 0.37705982 0.35137739 1.54211015 -0.08423593 -0.8595118 -1.1072458 1.75411782 0.91579317 1.05847124 1.52536833 -0.703220257 0.4891219 0.94531073 -0.02348034 -0.494945723
KEGG_STEROID_HORMONE_BIOSYNTHESIS 2.15700695 0.10244885 -1.53755271 0.84766905 0.5856113 -2.09650629 0.33261928 0.53843117 -0.6734007 -0.4685420 0.95573879 -0.82998047 -1.41476255 0.62639471 -0.09031677 -0.08950504 0.11011468 -0.44476912 -0.28512821 0.29866023 -1.98900643 -0.24411969 -1.43499147 0.86760041 1.02524276 -0.5932665 0.1374354 0.21201533 0.34436727 -0.41016807 2.07943956 0.425593065 0.3466719 1.06122025 -0.79768577 0.345420779
KEGG_OXIDATIVE_PHOSPHORYLATION -4.63240554 6.67049017 3.29453045 -5.55357439 0.5496431 1.77914583 -1.36568735 -0.24226839 -0.9307871 -1.1747541 4.67610019 -0.89434533 0.91778294 3.85769951 -0.94501694 -4.63557269 -3.61619441 2.54955115 3.68603811 -2.72776413 -3.86124115 -1.43398278 -0.68050376 3.04817148 -2.44714051 2.1306825 -0.6471011 -2.51904678 -2.43888735 -1.23953015 0.48985662 0.954496754 3.8663223 1.61356139 4.95225010 -3.050518657
KEGG_PURINE_METABOLISM 0.62601378 0.18764292 1.73576348 -0.39598650 2.8634149 1.74410636 0.80345344 0.21606301 -1.3228291 -1.6357118 3.37382979 0.50309725 -1.50193862 2.70460008 0.64046292 -2.91457181 -3.24668292 1.31429488 1.82156620 -1.17862270 0.22910565 -1.92894788 -2.19958482 0.95864285 -1.79749826 0.3013226 -2.0561912 -0.90114440 -1.30231555 -0.50822552 1.03537654 -0.062022288 2.3525705 0.47295983 1.48590730 -2.417920862
KEGG_PYRIMIDINE_METABOLISM 0.68740186 0.09101204 2.69635278 -0.42133976 0.8010248 1.80959049 0.21392008 1.07077719 -1.3103447 -1.9575492 3.30744108 1.47682356 -1.85296082 2.34519272 0.79412795 -2.39568143 -2.29502648 1.96378220 1.42298942 -0.45658368 0.59630261 -2.36440463 -0.67804226 0.66537108 -2.65018728 1.2139181 -2.3138877 -2.68945636 -1.24989873 -1.77690179 0.01581421 0.070503916 4.5215289 1.03102830 0.50944514 -2.892083563
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.40749755 -0.34200633 -0.67837708 -1.23839426 0.6450508 -0.87406128 0.89718094 0.88623623 -0.5901204 -1.4540001 -0.87199772 0.42565207 -1.02900922 1.09092642 0.83055385 0.95392316 -1.75399991 -0.70209561 2.56557133 0.74972926 -1.57575278 0.32540715 -1.39589409 0.64504509 1.67331106 -0.4742681 -0.4768781 0.84809297 -0.83978189 0.95527769 1.45671942 0.108438034 -1.0078854 0.58026404 -0.78212513 0.041770444
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 1.34480378 -3.30503462 -1.85282519 0.51114612 2.0581490 -0.56269049 1.33006959 0.04421460 1.1318004 0.3368706 0.50287384 -1.78230487 -0.50480571 0.94601805 1.04369734 1.71347618 -1.44995911 -2.43340216 -2.31170012 1.06556022 0.05794706 0.22204354 -0.97366673 0.37411217 1.72881970 0.3048721 -0.3882133 -1.42262378 -0.42158817 0.60165076 0.74800845 1.017367318 -1.4705719 0.31352222 1.51764940 -0.035286398
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 3.05533939 -0.89909141 0.10954792 0.57235547 0.4626350 0.43289545 0.80738496 0.82828340 0.3856202 -1.2192401 1.88574795 0.99850668 -1.58048436 1.26624831 1.63212252 -0.17105083 -2.04406219 -0.17476728 1.10667030 -1.31693777 0.48580641 -1.58414785 0.05762645 -0.83033135 -0.25313737 -2.7494190 -3.0328378 1.09278033 0.12945747 0.94310449 -0.20656930 -0.008758587 -0.5489564 0.03192254 1.53794235 -1.202205950
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 1.99685230 3.32822203 0.58345875 -4.52030235 0.3557779 1.04571821 -0.47089329 1.67689058 2.4018633 -4.7953730 4.07552302 0.75879243 0.62123432 1.51829109 0.78422115 -1.84905687 -1.97911844 -1.19127707 1.91957992 2.24311755 -2.31132941 -1.32123330 -1.89841999 0.56302584 -1.87052188 -2.8145421 -5.7964707 2.02162198 0.16550354 1.15166897 0.62682088 -0.514715091 2.6508192 -2.05463411 2.71049379 0.188390686
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 1.21309346 1.03875454 -1.40361861 -2.52868933 0.4749534 0.80310065 -0.98833939 -0.71560160 0.3172929 -2.7148765 2.17790950 0.73901374 0.25849033 1.55020704 1.20997178 -0.08496525 -0.53778049 -0.39412463 0.91390937 1.51429190 0.98942311 -0.15970919 -0.70389239 0.07882245 0.51719734 -1.0064894 -0.3389961 -0.74168366 -1.24385664 -1.12735156 0.43249880 -1.443631927 -1.1247770 0.97292321 2.74297956 -0.686449461
KEGG_LYSINE_DEGRADATION 1.27862971 0.71944399 1.63186710 -0.15625854 1.1239366 1.48957540 -0.71067310 1.03036572 1.0590009 -1.3259578 1.96846254 0.83164708 1.37283618 -0.32318559 0.82246557 -1.99572277 -1.13322958 -0.74814377 0.55359396 1.33240395 -0.03241343 -1.11966697 -0.40789253 -0.99695879 -0.31423848 0.5315305 -3.3596078 0.11542448 -1.01289512 -0.45023277 -0.42490054 -0.226806423 0.8458865 -1.67164998 0.99545026 -1.292086374
KEGG_ARGININE_AND_PROLINE_METABOLISM -0.15234479 0.69098240 -0.76904212 -0.91208540 2.2065375 -1.38716533 1.98078525 0.27213689 -1.1158975 -0.9181385 -0.25718855 -1.95804902 -1.12474003 1.25322167 0.53928573 -0.73049153 -2.14409282 -2.25112459 1.25901808 -0.05875601 -0.95521014 0.40928361 -2.08064840 1.77638819 3.15870419 0.6818472 -0.8337812 -1.63164697 -0.97781157 1.68806097 1.53083443 1.557264638 0.1741774 1.04524198 0.46754689 -0.433102466
KEGG_HISTIDINE_METABOLISM 2.68245243 1.47002186 -0.21440898 -0.53405078 2.0496709 -0.61763413 -0.26832178 -0.37983061 -0.5973106 -1.0657640 -0.90612550 -0.21298139 -1.00379460 0.17915007 0.94116346 0.18701698 -0.07179808 0.76376118 0.27104980 -0.74947548 -0.51319501 1.37082775 -0.09200211 -0.40229269 1.15117499 -1.9075314 -2.5648368 1.27744182 -1.25796002 1.29042314 0.68066731 -1.188354315 1.0593628 0.41174254 0.03668128 -1.274939998
KEGG_TYROSINE_METABOLISM 1.91319390 0.74537191 -0.21049549 -1.42486425 0.5137825 -0.64566994 1.25615471 -0.66586315 -1.0869967 -0.7914632 0.10529750 -2.04374233 -1.41200636 2.03136776 2.15096014 -0.71526488 -0.41213522 1.77566582 -0.93917591 -1.12144350 1.31645784 0.85531594 0.03889139 -0.64170442 0.13590477 -1.9150054 -0.9753372 0.62223967 -0.54517272 -0.39983433 1.31049742 -1.405758842 0.7396993 2.28797364 0.70968153 -1.156521954
KEGG_PHENYLALANINE_METABOLISM 1.71871162 0.85028780 -1.30449583 0.02082110 0.4768936 -1.66932255 1.68462411 -0.37651941 -2.3786373 0.7308768 -0.47484731 -1.97769588 -1.05075764 0.71056611 1.08003616 -0.61325382 -1.15603061 1.11546195 0.64651489 0.26703259 0.95952300 -0.67322170 1.09967677 0.27680080 1.06176322 -1.2410279 -0.2930592 0.65188967 -0.04065992 -0.62699333 -0.09001084 -0.001369905 -0.7343008 1.97832734 0.54187752 -1.169481219
KEGG_TRYPTOPHAN_METABOLISM 1.16300387 1.44923733 0.64807218 -0.54150723 1.8798625 -1.75904518 0.40200001 1.19892690 0.7528380 -0.8030061 -0.00259142 -0.37058216 -0.79497393 1.00982067 -1.00764660 -1.04581411 -0.91849620 -0.59010610 1.71370618 0.38679017 -2.82420827 -0.14129154 -0.09195268 -0.23903564 0.93135542 0.4710853 -2.9961143 0.43059167 -1.18463698 -0.21792140 0.89276830 0.137376030 2.7846734 0.56166925 -0.53510897 -0.749738309
> pickrellPar <- zscoreParam(pickrellCountsArgonneCQNcommon_eset,
+ canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esrnaseq[seq.int(min(nRowsToPrint, nrow(esrnaseq))),])
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 3.613776 -4.9679841 -0.49159131 1.17771731 2.7476858 0.9906586 7.8351036 2.3879352 -12.247507 5.1072799 -1.7088887 0.63969178 -0.43172043 4.310571 -1.08484087 -5.547877 1.76164051 -0.8898460 1.5516740 0.18384396 5.802682 -3.7757111 -0.84888911 -4.0044153 -2.8284060 -4.082546 3.4904554 -8.250833 -1.84490573 1.28570738 11.673596 -4.2948444 -3.9836382 5.0572394 0.389111698 1.27807521
KEGG_CITRATE_CYCLE_TCA_CYCLE 3.477784 -4.3258387 0.10679683 1.15022124 2.7107418 2.7378566 6.9986362 2.9781870 -12.336655 3.6489484 -1.0391481 -0.52824121 0.65826573 2.792346 0.29220725 -6.488304 0.72250541 -1.4678365 1.2401595 0.68473909 6.985360 -3.7270434 -0.23551620 -4.2369070 -1.5168679 -3.622173 5.4307235 -7.795052 -2.44363904 0.63072187 6.965976 -3.1341445 -4.1118426 6.2243145 1.240638472 -0.66792044
KEGG_PENTOSE_PHOSPHATE_PATHWAY 3.339370 -4.0330816 0.51583498 1.40649749 2.3302549 2.0374336 6.8119003 2.4065127 -10.353614 3.3243129 -1.0295482 1.11054456 0.15015971 3.222526 -0.22754631 -5.181391 1.31417726 -0.2722243 0.6939848 -0.36386838 4.818728 -3.5438041 -0.36599427 -3.3620882 -2.3822479 -2.812857 2.8927987 -6.781842 -1.39440389 0.65166045 6.613795 -3.4344536 -4.0261038 5.4529813 0.015849046 0.45574590
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 1.344052 -2.2158240 -0.21175907 -0.53842579 0.7156543 1.5288896 2.5831229 0.9317288 -5.466600 2.2964636 -0.8651491 -0.50386448 -0.91065031 2.898462 0.03623637 -3.073694 0.20949331 -0.2369633 1.4088917 0.05340645 6.570503 -2.3938190 -1.06915911 -2.4866369 -1.0079189 -2.759769 1.9916084 -3.275961 -0.49396629 0.49476943 5.002457 -1.8388175 -1.2006148 2.8157552 0.127652664 -0.45955629
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 2.631917 -3.4339405 0.76408579 1.94446913 0.3597460 2.0623149 5.8373764 2.2457127 -11.233068 4.4543105 -0.8609952 -0.10889232 0.29460916 2.556143 0.11638893 -4.873598 0.98963304 -0.2427547 -0.0727344 0.05007844 5.596166 -3.1119692 -0.66278612 -3.4164707 -2.3915290 -2.741625 3.6366017 -8.051503 -2.16851806 0.18545576 9.295116 -2.9409623 -4.3732252 6.2960637 0.230435983 1.13794800
KEGG_GALACTOSE_METABOLISM 1.982906 -3.9655472 0.61138910 1.15467260 1.6497432 0.8209315 5.2419040 2.1089802 -9.470991 3.7134731 -0.5181230 0.27522867 0.47877266 2.465661 0.52640555 -4.480509 1.01519660 -1.0516291 0.7645887 0.11440946 4.035460 -2.7583348 -1.29899318 -3.1760242 -0.7767365 -1.936233 2.8326448 -6.897092 -1.60000462 0.14907466 8.487595 -3.6464832 -3.5973961 5.0170353 0.116352490 1.61167165
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 2.062532 -1.7226116 0.04676367 0.09733945 1.3732660 0.6312735 3.1964202 1.1698729 -4.661225 3.5280417 -1.0282684 -0.24234280 -0.15789395 3.398797 -0.27367316 -2.285976 0.59113894 0.1038181 1.7998289 -0.70562100 1.466847 -1.9910010 -0.43593836 -1.5128138 -0.6582237 -2.253523 0.1210538 -2.828518 -1.52381952 0.63908058 3.312295 -0.9165812 -1.5677085 1.2962335 0.006141184 -0.07500485
KEGG_FATTY_ACID_METABOLISM 3.386727 -4.2988297 0.06235647 0.58211164 3.3131963 3.0678691 7.0037479 3.2012797 -11.277464 4.2927549 -1.4335746 -0.45941305 0.29576869 5.354193 0.02688667 -5.924900 1.13628254 -1.0545026 0.3870266 -0.12197680 6.536312 -3.4052486 -0.74006237 -3.1208879 -3.6370863 -4.832566 2.5697139 -7.724517 -2.04579965 1.96532286 8.388591 -2.7458801 -4.0057123 4.2475503 0.401532299 0.60919695
KEGG_STEROID_BIOSYNTHESIS 3.656540 -2.2721186 -1.57781964 -0.72604499 2.6915557 2.7253367 3.4859428 2.1396122 -7.766563 0.3563763 -1.7757330 -1.54337991 0.07930328 1.934096 -0.40859022 -3.366802 -0.91869676 -1.4728893 0.1800936 -0.22016331 4.432150 -2.6588099 0.96699753 -3.0431456 0.2835885 -1.981831 1.9816759 -5.436519 -1.29757797 0.75871060 6.245049 -1.8776229 -1.5097635 5.8384179 3.033017936 -0.93439173
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 1.116348 -0.9463790 -0.45604407 1.85063315 0.8106916 -0.3276203 1.2722726 1.5051284 -3.911297 0.4279352 -1.1991834 0.27030319 0.37304589 1.394388 -0.30774860 -1.744298 -0.92604666 -0.4823653 0.6953440 0.31728853 3.213363 -1.1520835 -0.44496503 -0.7902377 -0.8179018 -1.481037 0.8903110 -2.713066 0.11460137 0.99717578 3.970424 -0.9784062 -1.0879326 0.8027559 0.375701324 -0.63109969
KEGG_STEROID_HORMONE_BIOSYNTHESIS 2.480574 -2.2365775 -0.76345941 1.00478856 0.6737178 0.9885282 1.2763885 1.3246518 -5.234984 2.4601178 -1.4631961 -0.46795704 -0.10691565 1.885405 -0.83051072 -1.461525 -0.76902369 -1.9770725 1.6275719 -0.31312275 3.542358 -1.2925407 -1.34198406 -1.8121874 0.4845320 -1.476588 1.6850644 -3.134337 0.07214458 0.57869417 5.589447 -0.1789734 -1.8021160 1.3544518 0.029050681 -0.39441569
KEGG_OXIDATIVE_PHOSPHORYLATION 4.599553 -6.7100059 0.42751863 1.23309432 3.6403868 7.3503379 11.9441178 4.5820577 -22.111947 6.7108308 -2.6602605 -0.07351686 0.54111443 5.562369 -0.51723640 -6.354949 -0.32498263 -2.1480812 2.6116772 0.93083606 13.369164 -6.1648449 -1.26630351 -8.0783946 -5.1518001 -6.967977 5.0669407 -14.885391 1.28479521 1.01972315 14.812577 -5.0108056 -4.7390139 10.5574156 -1.074527837 -2.00447078
KEGG_PURINE_METABOLISM 6.220789 -7.3332881 2.16396498 2.57568871 3.9859659 5.9240050 10.3558058 5.7052135 -22.077635 6.8238021 -3.0415523 -0.54372207 -1.11552134 6.029539 -0.46629110 -7.154343 0.67053421 -2.8913745 4.9291899 0.29117744 13.403968 -7.1225909 -2.44539633 -8.3994983 -2.7797096 -6.288009 7.2046295 -14.113059 -0.82453646 2.33187623 12.429260 -5.8244919 -6.9103465 9.8373238 0.195600901 -1.74696832
KEGG_PYRIMIDINE_METABOLISM 6.251783 -7.3004492 2.45514238 3.55758788 3.5294787 6.1695147 10.5996032 5.4341495 -20.035750 6.8378927 -2.6453473 -0.25241143 -1.71619115 6.033213 -0.02466917 -7.150940 0.78178056 -2.2034922 2.5335758 0.25118554 10.327172 -6.6221964 -1.55381413 -7.3268938 -4.5723746 -5.782497 6.6734213 -12.451852 -0.73080869 2.09920973 9.852821 -4.1746574 -6.4184518 10.0207656 -1.585732321 -0.85976870
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 2.224928 -2.5175231 0.31954322 -0.05577043 3.0724152 2.4451896 2.5921602 2.1124348 -8.210483 2.8724531 -2.1070978 -1.60741186 -0.68246497 2.199909 -0.19364540 -3.650181 -0.42907746 -1.8261277 3.0553026 0.60745873 8.136535 -2.2790936 -1.58939303 -3.1084949 -1.7070042 -2.761089 3.4866388 -5.033765 -1.82076593 1.96304371 5.189870 -1.6042160 -2.6184510 2.5338460 1.312164296 -0.32183720
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 2.999856 -3.4375039 0.89916682 0.63033836 2.4687629 1.9603347 1.1901481 1.6342611 -6.972969 3.0118818 -2.0881152 -0.72779749 -1.62320621 3.334605 -0.62335248 -2.686378 -0.91324037 -2.4721889 2.3887953 0.02658081 6.061305 -2.0460961 -1.20709007 -2.7982678 1.6860733 -2.621328 2.2711386 -5.897327 -1.23629767 3.63007666 3.537552 -2.4197078 -2.4758398 2.1078716 2.260659728 0.14729905
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 4.528253 -4.1049604 0.95473848 2.35554742 2.7822856 2.4088547 4.0580919 3.0774039 -9.706246 4.2374134 -2.1616616 -1.01364410 -0.94299011 4.890240 0.03792379 -4.658464 0.24416843 -1.9253826 1.9851437 -0.79513338 5.959851 -3.1596842 -1.27828378 -4.1484755 -0.6797800 -3.179783 2.6697157 -6.646975 -1.44841945 2.43818842 4.976755 -2.7140771 -3.0367858 3.6516496 0.249454763 0.09506715
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 3.578068 -5.2126760 -0.06582990 1.05028056 3.1175359 2.9255891 8.6648883 2.3315356 -13.262600 4.3087913 -0.4353979 -0.65613429 0.66965563 6.611628 -0.05894749 -6.337658 0.72653584 -0.9627796 1.2156060 0.23131911 7.440367 -4.5184377 -1.26578230 -3.5938565 -3.1877200 -4.678520 3.2011377 -8.745689 -2.57894300 1.66411861 9.113690 -3.2824421 -3.9956024 4.9755314 0.821735158 0.19100324
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 2.540325 -2.5580006 -1.05293097 0.95062670 2.7166826 2.4195780 2.5974731 1.1984907 -6.563815 1.1393911 -0.6535133 -0.53905503 -0.48018704 2.677603 -0.01257593 -2.979565 -0.07920138 -1.4780887 0.6527642 0.82805025 4.578221 -2.3827049 -1.46480651 -2.3355377 -0.5622099 -2.138416 3.8006165 -4.314880 -0.76030110 1.13881051 4.554075 -2.4839790 -2.0330791 2.0076049 0.891015248 0.18152038
KEGG_LYSINE_DEGRADATION 3.602131 -5.1825796 2.10404410 1.03465213 2.2325113 3.8859631 6.2068738 3.2557411 -13.475952 4.4676256 -1.5475372 -0.64332512 0.30278276 3.096102 0.80316244 -4.861363 -0.16047923 -2.7961166 3.1711096 0.15946804 7.862459 -3.9302227 -0.46045256 -4.2726251 -0.8764999 -3.201900 3.8283383 -9.229505 -1.76236481 0.80665042 7.238060 -3.3994653 -5.0360166 5.6878045 1.220045863 -0.12912036
KEGG_ARGININE_AND_PROLINE_METABOLISM 3.552908 -2.6014549 0.25403717 0.44467074 2.9611366 2.7482330 5.2593925 2.8596838 -11.003736 4.4014280 -1.4301706 -1.48503133 -0.53070060 4.554944 -0.84220810 -4.833547 0.25503808 -1.8556128 2.1043602 0.08116681 7.166741 -2.6433864 -1.27027071 -3.8686066 -2.0615804 -3.311451 3.5978009 -7.755397 -2.32827010 2.16085780 7.856669 -2.3568083 -4.1579194 4.1342672 0.563638193 -0.62082177
KEGG_HISTIDINE_METABOLISM 2.377756 -1.5661914 0.96968517 0.67672158 0.9721192 2.3359869 3.2557159 1.0090144 -7.185205 3.1549802 -1.8899941 -0.60468775 -1.07159899 2.157091 -0.57746861 -2.782320 0.04684621 -1.1830784 1.5261956 0.19975447 3.864136 -1.8653606 0.09025289 -2.5738520 -0.6662499 -2.626624 0.5408687 -4.116989 -0.76704574 0.94226265 5.226687 -1.5137978 -1.9567396 3.5069890 0.784552904 -0.69041273
KEGG_TYROSINE_METABOLISM 1.678686 -2.8624559 0.11380858 0.96294524 0.6770510 2.7615384 3.4725219 2.3537463 -8.530014 3.5068974 -1.7874306 -0.61405904 -1.40109143 1.614691 -0.66315954 -2.873058 0.36251656 -0.9941132 1.1490792 0.76083067 7.367480 -2.0494605 -1.01357494 -2.6154799 -1.7935798 -2.941109 2.5428844 -5.886190 0.22349847 0.56447214 5.669252 -2.2344264 -1.0213345 3.1941475 0.652568301 -0.34807790
KEGG_PHENYLALANINE_METABOLISM 2.090906 -0.6398089 -0.96814219 0.10793026 0.9964645 0.5346435 0.6255186 1.3708515 -4.156439 0.9251142 -1.8077444 -0.76133326 -1.10126175 0.105535 -0.33588778 -1.258697 -0.35343074 -0.9379906 2.7207387 0.00165670 6.070485 -0.5640568 0.14502636 -1.1017496 -0.7081219 -1.161937 1.3090258 -2.597788 -0.49159141 0.02963533 1.589456 -0.9849399 -0.2852917 2.7296313 -0.251299048 -0.88510761
KEGG_TRYPTOPHAN_METABOLISM 2.427252 -1.8565270 -0.36746740 0.32340813 2.1446252 1.8352479 4.3807816 2.0802495 -8.862574 3.1187773 -1.1165949 -0.32613518 -0.01228540 3.252853 -0.62866265 -3.014655 -0.48220328 -1.8893938 2.7605496 -0.83247782 5.133392 -2.3976572 -0.27716429 -3.1951290 -0.5176048 -2.990382 1.8257622 -5.044709 -1.80260786 0.91193140 5.959211 -1.2696260 -2.5846251 3.4311657 0.932687520 -1.04941279
>
> gbmPar <- zscoreParam(gbm_eset, brainTxDbSets)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up -0.08909934 -3.152221 0.8107079 -5.2069957 -1.033834 -3.508842 -3.1829696 -0.6973523 2.015886 1.1632330 0.8404895 -2.159491 -2.548436 -0.8250184 -3.4106404 -4.002532 -4.613817 -3.044947 -5.242683 -1.2277799 -2.5902555 -3.9951172 -5.281595 -0.1906933 1.3229285 -2.3332362 2.2376210 -1.582096 -3.701165 -1.7871696 0.1453581 1.3152286 -0.9330403 -3.939937 -3.847457 -2.256774 -3.6583197 -3.343534 -1.732189 -0.3798295 -3.595637 -2.2691422 -3.4280276 -0.6868929 -1.5292866 -3.6440129 -0.8287959 0.4759527 -3.1435814 0.6136584
astroglia_up -3.10555037 -7.101899 -4.0708334 -9.6701263 -3.664210 -5.299715 -6.9344991 -2.4056788 2.838336 -4.0490130 -3.1252581 -3.831245 -2.365279 -7.0701428 -1.7311405 -3.642857 -9.353379 -6.868324 -6.498363 2.5117857 -1.8454742 -8.1922252 -8.284021 -8.5971607 -0.8126084 -2.3739610 0.8329655 -4.621603 -7.722374 -6.1625899 0.7790239 0.7748605 -2.9931959 -2.105014 -4.057559 -3.331656 -3.4418359 -4.645598 -3.835184 0.7608445 -4.037412 -3.3140937 -8.1346699 0.6228006 -1.9891070 -3.3462253 -1.0731883 -1.4644452 -5.1808878 -2.8928713
neuronal_up 7.37537036 0.902553 0.3057596 0.2300378 6.512670 -1.073758 -3.5261610 3.0524882 3.747227 0.1086332 7.3042698 -5.441629 -4.460294 -4.1315377 -0.9454844 -3.971821 3.422017 -4.541850 -2.411690 0.8123934 1.3326064 1.2388876 1.226472 -1.2244988 -1.4490155 0.2784605 5.5226593 -3.202053 -3.079236 -2.3312546 0.4439339 -0.4968675 2.5700910 2.587650 4.151428 -1.103735 0.1977171 3.893207 1.635213 -0.4158050 2.809088 -2.6602840 3.1488241 3.7441383 -0.2328512 -3.6994980 -3.8924016 8.6663741 -1.6945566 0.3744679
oligodendrocytic_up 3.29318629 1.254525 3.2712757 2.7191887 5.272348 1.175787 -0.2208184 3.3361411 3.463337 -0.8905276 4.5060174 4.925995 9.254130 1.6478948 -2.4138339 2.381934 -4.283642 1.802069 2.652757 0.6540577 0.6721184 -0.2149802 2.097069 1.0987993 3.9911220 3.4783625 5.9792216 1.707458 5.240817 0.4118169 2.0783070 4.4474700 2.4108206 4.348025 1.816250 5.848493 -0.1675866 3.913055 6.890191 -0.1129943 2.247621 0.3634295 -0.8202027 3.2955322 5.6991646 -0.6973273 0.6332216 0.5563794 -0.7722805 2.2257859
TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up -4.0501595 -3.58528280 -2.150553 2.6903341 4.4208691 8.164340 2.1478449 2.838322 2.5975997 0.37673200 2.838609 2.075690 3.310031 1.3772906 4.1679206 3.366810 1.771455 1.1231341 -0.3661421 4.8202400 1.8597821 0.2832633 -3.299052 0.4615451 2.080973 0.75936460 1.128923 1.91788210 3.565186 2.8923945 1.620005 3.9857385 2.1520939 1.5575374 1.4959032 4.756540 -2.867930 -0.6443480 0.85949798 -1.785971 -1.176208 -0.7720236 2.199689 -0.4467583 -0.06920086 -0.1063925 1.59512455 0.2113819 2.180979 1.594056
astroglia_up -7.8449103 -3.69159341 -5.755313 3.0432536 -0.4214884 3.141192 0.4343735 1.984018 -0.1593382 0.03139333 -5.837569 -1.925856 -5.373983 -0.4965235 0.8055162 1.604746 -1.688300 -0.5820614 -5.4221591 -1.9257791 1.7990137 -1.8344248 -5.126051 -2.2978494 -3.971752 -0.08022663 1.269094 -0.04203954 0.291440 1.2673922 -2.484940 -1.8906992 -0.3366926 0.1137957 1.2937214 3.049417 -1.620135 2.3199253 -0.15299389 -4.373301 -3.517849 0.7444723 1.008946 0.7440944 -1.30587497 -1.1595379 -0.12211222 -0.7345510 -1.016347 -2.525468
neuronal_up 0.7621561 -1.58714007 3.908310 5.1544726 -2.8583933 6.461310 2.4198545 13.914963 4.5975953 1.16075755 26.315151 6.131003 28.314920 0.9021609 2.6534158 10.109527 -1.392535 2.0200464 12.5550187 1.4292865 0.5672497 2.9720049 5.488963 -1.8932872 22.021493 4.08113876 1.624494 4.29047134 1.231357 1.0326487 -6.201044 3.2394715 -4.5485246 3.5140611 0.8060133 -2.388428 -5.656942 -5.3246569 -0.02576302 -2.989774 -2.180673 -2.7829681 -1.709889 -4.0113452 -5.27955635 0.1081630 -0.65506207 -5.1568867 -2.899157 1.900477
oligodendrocytic_up 3.4473515 0.08207331 2.122737 -0.4139425 -3.6839021 1.784584 1.6375784 3.111439 -1.1400225 0.24599609 2.236097 -1.539376 1.530867 1.2539415 1.4258764 3.523489 -2.181047 -2.2383685 -1.0576358 0.2384092 4.2246382 -0.1492978 -3.327585 -0.7908182 2.860221 -1.23331168 -1.455083 -1.56496385 -2.848318 -0.4789735 -1.910726 -0.6964973 -0.9156850 -3.7150977 -0.1130542 3.021765 -1.968815 -0.8635538 -2.90146119 -3.962522 -4.266302 -1.8826848 -2.813841 -3.7335868 -2.67976967 -3.3860511 -0.08389153 -1.4103498 -1.328776 -1.187159
TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up 2.676893 4.30587603 -0.1484128 2.121824 1.193762 0.216868 2.098520 -0.3590077 1.4924973 3.1318506 -1.885732 1.708314 2.657195 4.545553 2.912760 1.9804288 3.802850 4.534642 -0.003929236 3.2517485 -2.888534 0.1771372 -1.1738971 2.8936005 -2.743719 1.2918124 0.08247081 -1.203403 1.4767707 -0.304507 -2.321400 -0.4437532 -0.3035455 1.4292700 0.6915937 4.0222928 0.19722388 -4.5950920 -0.9341628 0.3305044 0.1631184 -2.8586504 -0.5955305 -0.2539437 0.8313484 1.589897 -0.7911376 1.293819 2.079665 0.9014619
astroglia_up -1.410315 0.04597652 2.5770285 2.311639 -3.398351 -1.272882 2.373027 1.6009710 -0.2377814 -0.0469951 -3.575104 -3.168532 2.258187 1.899525 1.815670 0.1310026 -0.363329 3.570761 8.762186646 3.2915183 6.806357 6.3444795 5.9779424 5.6455262 2.528754 3.0563019 8.59482813 2.857618 5.3890853 3.179268 3.523551 3.7860581 3.8898683 6.9126141 4.3234965 7.5338826 4.60504082 -0.2121851 4.2592086 3.3834519 4.3762196 5.9914008 5.4677275 2.1915212 6.4911546 2.848080 -0.7855700 4.469387 5.496258 2.8326382
neuronal_up 2.935035 -4.33202655 -2.3779648 -4.899466 1.924114 -2.897353 -2.767796 -3.8811350 -0.3370994 1.1164572 -4.545340 -6.060301 4.539371 -3.571778 -5.669859 -2.6699004 -3.006828 -3.455450 -1.900261556 0.6429803 -3.745943 -4.3142406 -2.7433338 2.6788158 -2.270892 -1.1439441 1.03773052 -2.029232 -6.1026313 -3.833959 0.559603 8.2443008 -2.5442885 -0.3626451 -2.5297864 -0.5810968 -2.26408321 0.6219462 -2.1951042 -3.4844647 -2.0629756 -3.2574162 -4.6249237 -4.2837280 -2.9083139 -2.304073 -4.9578554 -3.231750 -2.616099 2.6652850
oligodendrocytic_up -1.429602 -1.16836372 -3.3273872 -1.484285 -2.102452 -3.335235 -1.695018 -2.8550582 -5.1228981 -1.1518311 -4.754625 -2.497824 -1.200832 -3.091723 -2.826340 -2.3319305 -2.020322 5.901598 -1.869680552 1.5415212 -1.287606 -0.8869270 0.6441386 -0.9799234 -4.562924 -0.1648678 -2.00977500 -3.914152 -0.6328189 -1.448776 -1.641520 4.8529785 -1.1013767 -0.1757191 -1.5306714 0.6552283 0.05824521 -1.7220446 6.6503840 -0.2605514 -1.7376517 -0.6012265 1.1494110 0.9321423 3.3145489 -3.385071 -3.7834245 -2.604791 2.660582 1.3763185
TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up -1.5182935 1.414137 0.6145721 1.3611626 0.9299387 -0.6118263 -1.9077298 -2.977643 2.354636 1.256214 -1.0446336 -0.03521543 -0.2048689 0.08255436 -0.5703374 -0.5160375 -4.393404 -0.04869947 1.0193142 1.716183 -3.050138 -2.968484 -1.4182898
astroglia_up 3.6679577 2.016040 3.8365848 5.3857249 3.6519214 4.1911267 2.2371880 2.996960 3.653019 2.850722 5.3799630 4.07607902 4.5965300 3.82064210 6.8146847 2.5472498 2.787112 3.48964654 3.3631687 7.909505 4.609892 2.788675 1.2952133
neuronal_up -3.5923614 -2.462081 -3.0230934 -2.2989952 -2.9441875 -2.8335093 -2.8902359 -2.778339 -2.445036 -4.896693 -0.7803416 0.16600660 -2.5170378 4.64377108 -4.2430666 3.5077554 -2.229394 0.68892787 -4.1220154 -2.572970 -2.437011 -4.344700 -3.5499763
oligodendrocytic_up -0.4309207 1.205395 -3.3004554 -0.2007412 -2.3954090 -2.6221966 -0.6024445 -1.075083 -2.183149 -1.983176 -0.3895268 -0.45898726 0.9638120 -1.89896706 -1.4509535 -0.1200174 -4.067190 -1.98215669 -0.5922569 -1.755122 -2.906155 -3.149109 -0.9366359
>
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> leukPar <- zscoreParam(leukemia_eset, cgpC2BroadSets,
+ minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP -2.3189547 0.55622710 -3.11198172 1.4986887 0.79561210 1.27047787 -0.65748275 -3.6475523 -0.938530423 -2.2124263 1.492202601 -0.73476415 1.14702413 -1.8556094 -0.10710987 0.62555189 -1.84985291 -1.99696364 -1.6391298 0.7733034 -0.76199840 -0.11481253 -1.54473797 2.90988107 1.91589932 0.306170802 1.84065500 1.0454556 -1.7550145 -0.64379309 3.1809700 1.66381825 0.85600132 1.5031001 5.27303344 -0.3741954 -2.3891628
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP -0.1437327 1.34145819 3.12030398 -0.9451609 -0.65236606 -0.75734866 2.49198413 -0.6960575 0.479216286 4.2298075 1.699907478 1.80608946 -0.55495287 -1.2596018 0.67756954 -0.22151006 -0.57450357 0.22116396 -1.9389978 -1.6951874 1.38964755 -0.02115285 -0.93820411 -0.54585990 -0.77666967 0.094771714 -0.46941562 -2.4584473 -3.2781747 -0.41248115 1.9550954 2.96291598 0.77692080 -1.1198979 1.01968846 -2.1157809 -2.6910370
WINTER_HYPOXIA_UP -2.2032116 1.94192756 -1.01905531 -0.2262124 -1.70570515 -1.31370553 -1.53784382 -4.1896689 -0.573056157 1.3188203 -1.630985843 2.11056496 3.86978019 1.7943601 -3.47417711 -0.09511845 -1.03683603 -1.41318482 -2.0541609 -2.5022841 0.95884756 1.99489650 0.01912947 -0.40707157 1.49731005 1.876664626 0.82794692 1.3034511 -1.9570481 1.23100844 4.5355537 2.45428354 2.43716611 -2.4481408 1.95214281 0.4155076 -2.7518949
PYEON_HPV_POSITIVE_TUMORS_UP 1.8425924 -0.90371747 4.42311845 -3.7133346 1.07235312 1.59420262 1.54184230 5.1765404 4.512483991 5.3940779 0.528141105 6.86588624 -5.27763956 0.5196579 2.48547689 -1.84517673 2.66475634 3.44169814 -0.7470868 -5.1281340 -0.05626604 -1.23659933 0.25586378 -3.15164039 -4.16550799 0.041309197 0.47627197 -2.3210603 0.1246063 -5.22630542 -2.5795122 3.27132937 -0.03055620 -2.0519735 -3.90153690 -3.1462161 -0.7499449
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP -2.0355786 2.60368733 1.65952935 -0.2731903 -2.82481184 -1.60635471 0.40429957 -6.5356063 1.373085999 3.2217230 -0.004117969 3.12303563 1.37715940 4.3192977 0.04425356 -1.21708631 -2.06097063 -0.94940011 -2.9791103 -4.4507436 1.15163993 -2.13360896 -2.04857971 -2.73828950 3.09070632 0.890670934 -2.19450875 1.7569005 -2.1019689 1.35470426 5.2654387 2.89066529 3.53097016 2.9110126 0.45673634 -0.7116174 -4.5599727
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP -6.1743193 2.10626458 -9.93033191 5.5020838 1.24528029 2.76706915 -0.76977556 -10.1318343 -1.226965247 -0.2985038 3.204167870 -2.06583449 4.01539216 -1.4989300 -0.80243199 -2.09676668 -3.92339728 -4.76956131 -3.5492403 0.6307940 -6.10750595 -0.36445017 -5.33447764 3.97968003 1.06375876 -1.501968354 4.59460616 3.0050082 -5.2099545 4.59692879 8.4071865 3.02679350 4.62088574 4.2776647 8.40747357 2.6954767 -2.3902658
LU_TUMOR_VASCULATURE_UP -2.3516037 0.23422156 -3.24709239 1.9002877 1.06371531 -0.31124003 0.64150436 -4.4921642 -0.429394270 -0.4708068 1.209418772 -0.53680406 -0.18120399 0.1020756 -1.17510637 -0.13495767 -1.60844266 -1.61180192 -0.2395109 1.6463378 -2.91072538 0.28004166 -1.85054840 3.12872425 0.81025980 -0.427636238 1.02779187 1.5058078 -3.8168552 3.69953701 1.2982542 1.83497935 0.73751145 2.3115023 1.90714553 1.9502801 -1.4935021
KORKOLA_EMBRYONAL_CARCINOMA_UP -2.0102420 1.77944838 0.71764392 0.7225229 -0.47650814 -2.94754400 -1.68662524 -2.7193614 -0.282629306 0.8789733 -0.663623433 2.48363943 0.58547469 0.9084250 -1.30090891 0.91028023 0.22038861 1.58879655 -1.9871067 -1.0238739 2.48127825 1.11685683 0.80172070 -0.88055998 -1.02367666 -0.170070225 -0.56110595 0.9707670 -0.6937145 -0.51027108 1.3912644 1.21188680 1.78787521 -2.5882821 0.35238902 1.0686185 -0.4521463
KORKOLA_TERATOMA_UP -0.3532193 2.17997348 0.03956106 1.3024658 1.85511030 0.23121185 -1.71392644 -2.2452103 -1.891420902 -1.2620777 -0.745760801 -1.54879367 -1.14580035 -0.4412586 0.13971105 1.04541604 -0.18902172 -0.56554466 0.0430148 0.3175348 1.08482965 0.62953613 0.19987932 1.49131527 -1.44961377 0.238083305 1.05678681 1.2490852 -0.7551186 -0.06277113 0.4286523 0.11269812 1.05268675 -1.7303152 0.59079381 1.2819498 -0.4704426
KORKOLA_YOLK_SAC_TUMOR_UP -0.1040637 2.99594415 1.31530981 -0.3081178 0.62832670 -2.42448384 -1.00992574 -1.6262212 0.163843219 2.4035673 0.155357913 2.06606337 0.24037257 0.4130723 -1.10335321 -0.70220925 0.89210405 1.60172761 -1.0474659 -0.7906492 1.09211241 1.15544503 -0.36703662 -0.60395345 -2.57074459 -0.583146941 -0.73629462 0.3110249 -1.7065781 -1.25258365 0.9935598 0.79136836 1.51933857 -2.7892840 -0.09963966 1.6070600 -0.5198466
KORKOLA_CHORIOCARCINOMA_UP -0.3744594 1.47839993 -0.77812840 -0.2217174 0.83857394 -3.22690712 -1.70821076 -1.8247392 -1.096790972 0.7766130 0.106430602 1.53596539 1.48267931 0.3337191 -0.10364576 0.33957176 0.78113867 0.08030119 -1.7081769 -0.9363552 2.19093776 2.26944769 0.71838354 -0.24247756 -1.29633819 0.701466602 0.09347977 1.4125416 -1.8054660 -0.61006004 1.4158132 0.45544767 0.58758936 -3.0940532 1.23411751 0.5310415 -0.3361331
KORKOLA_SEMINOMA_UP -2.9340089 0.09586312 -0.67073745 0.4686024 0.58281055 -1.86617285 -1.39432462 -3.8666739 1.166840265 1.9282066 0.806977219 2.90705383 0.99184039 0.1234681 -0.96569590 -1.16396240 0.28761478 2.57697201 -0.8848146 0.8255735 0.58071491 -0.18386443 -0.64027729 -0.33107070 -2.65069999 -0.739030827 0.26850943 0.6218152 -1.5319993 -1.03372781 1.5970938 1.42233007 2.14424171 -2.9444395 2.36223981 2.5275209 -0.4847880
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP -0.1871021 -2.72933254 2.10389786 -1.5218035 -0.24851512 -1.94879594 -0.11225920 1.3387953 2.092476554 -0.5027557 -0.734496247 1.48332203 -2.06908392 2.1504269 1.57346111 -2.67286549 0.55601780 1.75728633 1.0591640 -3.5172751 0.41769901 -0.15799519 0.10733345 -1.26412040 0.62132681 -1.068445939 -0.81184190 1.7795510 2.8672636 0.51834308 -2.2301655 -1.72721639 1.30982203 0.7498270 -2.26434985 1.7641941 1.5182121
HOLLMAN_APOPTOSIS_VIA_CD40_UP -0.7820872 -2.13675642 3.39698951 -2.1548508 0.90823798 1.87534780 1.18216325 -0.3454263 0.519486282 0.7495966 -0.702832818 2.65768682 -1.39601416 2.9377153 0.01460505 -3.73008343 -0.30955544 2.04220857 -2.8652428 -3.1013878 0.38820637 -1.85976238 0.14583211 1.54497828 -0.51769728 0.030388041 -1.27655961 -0.1068228 0.1140717 0.19735404 -1.8393420 0.06094494 1.18064262 1.7171987 -0.09629675 2.0372182 -0.4801540
LIU_PROSTATE_CANCER_UP -2.7418994 0.36658204 -3.31691584 1.3184501 2.30781570 0.78372138 -2.49394355 -5.4987675 -0.822790802 -1.2417137 0.174898665 -0.25341599 3.10520813 -3.4272596 -2.36564481 -1.46486084 -3.27025426 1.45149707 -1.9796783 -0.2385052 -0.10360642 0.41913964 1.31326282 2.25499078 -0.48834592 1.569427440 3.08573035 0.6747347 -2.1158608 0.88924255 2.5723039 2.39831139 3.32890627 0.5872895 3.74319390 1.1868815 -1.7081250
LIU_SOX4_TARGETS_UP -0.3751389 -1.95588700 -0.83556096 2.8406515 2.03541886 1.67651015 -0.06264359 1.0278755 -0.621726452 0.1542651 2.093682904 -1.12917548 -2.22483713 -1.1771779 1.46468782 -0.49621654 -0.06320445 -1.49441905 1.4408110 1.3723181 -2.65175416 -5.32222009 -1.90422195 1.32712098 0.41560025 -0.141050306 0.65594298 -0.6743251 0.5105999 2.58778466 -1.0269048 -0.06555656 -0.16265033 2.7736846 0.23669453 -0.9452083 0.7162302
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP -1.2464061 -2.52190564 0.34481699 0.6136117 4.14525942 1.31851001 -1.50928145 -3.5261653 -0.376143666 -2.1419889 0.263685045 0.03051013 2.23927375 0.2887824 0.30432686 1.08666353 -1.81678277 2.91665062 -0.4815280 3.7840202 -1.28255238 -0.92708160 -1.47494702 0.36348866 -1.35695710 -1.365236115 -0.09332459 0.6773143 -3.3005646 1.08982967 1.3469267 -0.15650030 1.18988291 -0.1304936 -0.41848104 5.7424208 -3.6196334
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP -3.8776379 -1.06789926 -7.00642158 5.2446555 1.06812916 1.14091106 -1.23350873 -7.0151593 0.787783143 -2.2876206 4.506629996 -0.82513916 -0.50395314 -2.3986535 -1.14874866 -3.70233709 -0.71755286 -1.99280231 -1.4519194 1.8781710 -5.50515340 -3.26577909 -6.14460283 3.77798602 1.26457017 -2.522562013 2.00592405 2.4181014 -3.8502790 6.01626665 3.2565317 1.33592939 2.78983801 6.8105203 5.47203316 7.8148200 -1.0710708
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP -0.5530494 0.91449001 -5.10684798 5.8892478 0.70327111 0.68010952 -1.35401240 -4.1731715 0.829970887 2.0186035 0.734848132 -0.53350919 3.00824815 -1.7128629 -2.31656387 -1.10739140 -1.78453464 -1.33346346 -0.1610865 0.1636164 -4.61596682 -0.04388835 -2.22820486 3.50293537 1.08838500 -0.856531524 1.18347365 0.7537940 -3.2931554 -0.12534415 2.1550084 1.22544443 0.02188584 3.0547016 4.00283815 0.7785386 -1.4098262
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP -1.0842740 1.15191033 0.19359086 -0.2177736 -2.01743872 -0.35397625 -0.86551082 -0.6587418 -1.482192451 0.5834861 0.095377824 -0.80250318 -0.03850151 0.1414836 -1.48102277 0.70702073 0.54101179 -1.89001468 -0.1428820 -0.2992931 0.06876902 -1.27262670 -0.73299530 0.15317029 -0.21894175 -0.995729217 0.31049138 1.3867304 0.8623611 2.09995277 -1.6338695 0.65923937 0.40301566 2.6698444 1.87944620 0.4256969 1.8556888
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP -0.6904303 1.93458550 -1.99458125 1.5799006 -0.04746809 1.35845690 1.35954571 -1.3239543 0.183594189 -0.7304046 -0.867718542 -0.16037922 1.01551852 -1.2458131 0.36381625 -0.77975659 -0.36807781 -0.37384028 0.5956824 1.1883224 -0.48945985 -0.09633758 -0.76459822 0.07532145 -0.07071889 -0.592753031 0.03215539 0.4208453 -1.3262166 0.06108885 1.8490292 -0.26820419 -0.03938847 1.1315785 2.00315374 -0.7778437 -2.1446504
FRASOR_TAMOXIFEN_RESPONSE_UP 0.5413132 1.28746036 1.36441186 3.3368271 -1.31891545 1.57406315 0.31091232 -1.8851886 -1.508855984 -0.2751830 -0.859463551 -0.54855067 3.08124648 -2.9190068 -2.21050219 -1.68670629 -1.28382294 -0.29745413 0.4018516 -0.7913413 -2.31590360 -2.18097162 -0.89954411 1.44692469 0.04672709 -0.343429133 0.79945007 0.2049267 -0.4953848 0.11145147 0.2050700 0.26420024 0.55065832 1.2372609 3.15265775 1.3700061 0.5328047
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP -2.6864978 3.43756903 -8.37492717 3.4513206 0.39310486 2.00425397 -0.88377471 -6.5962386 -1.122346365 -3.3992922 1.699856481 -1.83778409 1.82943931 -1.0046215 -2.58511818 0.68047190 -2.39298391 -4.23623360 -0.4038435 3.2643617 -5.42149983 -0.47681907 -2.08912701 3.41957446 0.43726984 -2.000731185 4.26612070 1.7425539 -3.2522439 1.90242944 7.7104250 1.33084413 0.94700410 2.9575476 6.54983238 1.8646617 -1.1245584
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP 0.7708646 1.64610911 2.90389826 -1.5098526 0.68514559 -0.62856125 1.44344048 -3.6093879 3.733916242 5.8656510 1.554307033 3.80813115 -4.74817478 0.9967577 4.21335589 -3.79160251 -0.27816578 2.15737725 -2.0032367 -3.5666508 -0.60209057 -1.95764050 -4.09387535 -4.91121565 -1.31860793 0.004839387 -0.71339502 -0.6991190 -3.9212620 0.20648249 4.1143265 4.94718475 2.97327802 4.4147432 -1.74889853 -0.4990265 -5.8390450
WATANABE_COLON_CANCER_MSI_VS_MSS_UP -1.7007583 0.25210547 -2.98028816 4.3616661 0.78884983 0.07233832 -1.40118606 -2.8961949 0.004100867 -1.1888170 -1.104752765 -1.38781767 3.19210792 -1.1626383 -2.68443406 -0.86437807 -0.25770287 -1.21047088 -1.4287985 -0.5138995 0.58785731 1.62059758 0.58826582 2.11523939 0.95256194 3.100843936 2.98714276 -0.5977086 -1.5766500 -1.05054331 1.8346936 -0.50176549 0.33463179 0.9073378 3.12400300 -0.2618967 -2.0536422
>
> proc.time()
user system elapsed
51.87 6.26 57.87
GSVA.Rcheck/tests/test_zscore_newapi.Rout.save
R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> ## 2023-11-10 axel: simple test script for method z-scores, new API
>
> library(GSVAdata)
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
table, tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: GSEABase
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
expand.grid, I, unname
Loading required package: XML
Loading required package: graph
Attaching package: 'graph'
The following object is masked from 'package:XML':
addNode
Loading required package: hgu95a.db
Loading required package: org.Hs.eg.db
> library(GSVA)
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2023-11-09)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 1.4171739 -1.3444519 -0.99052898 0.4203395 1.30716224
g2 -0.7281951 0.1814902 -0.64652976 -0.8254491 -1.08420520
g3 -0.2667018 -0.3726754 0.09779699 -0.6792548 -0.09124045
g4 1.0735382 1.3156255 0.15588330 -1.8079608 0.48531108
g5 0.7229884 -0.9162342 1.93982245 0.1503313 -0.45893601
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> zscorePar <- zscoreParam(X, gs)
> zscore.es <- gsva(zscorePar, verbose=FALSE)
> dim(zscore.es)
[1] 100 30
> zscore.es[seq.int(min(nRowsToPrint, nrow(zscore.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 -0.397989121 0.63767552 -0.71152962 0.95681431 -0.39154705 -1.0418650 0.76943162 -0.22652269 -0.03794476 1.23795689 0.54741085 0.541307906 -1.3025217 -0.07350935 0.5617042 -0.110558260 -1.48434203 0.48341124 1.4582348818 -0.6596565 0.42366570 -1.18733982 -1.38666349 1.77213207 0.49521884 -0.54625805 -0.46923643 -0.326809131 2.03448230 -1.565153279
gs2 -0.292150055 1.00652251 0.59082177 0.60360826 0.09399124 0.3990216 1.16059005 -0.51857868 1.57864006 -1.82507931 0.27951753 0.015075493 0.7420740 -0.26993044 -0.1951051 -1.228360534 -0.29127936 -0.38907836 1.7217817461 0.4289776 -1.05871842 -1.92619800 0.16799779 0.27006041 -0.01617003 0.22027905 1.62510577 -0.140877183 -1.58374028 -1.168799069
gs3 0.286561399 -1.05214008 0.44954052 0.05225134 -0.27816203 0.5745265 -0.08816684 0.55254769 -1.29875323 1.56194900 -0.05237899 0.263111063 0.9526169 -1.98894869 1.9629224 -0.260586823 0.03510070 0.11049165 -1.0053564642 -0.7887344 -2.62545010 0.37942785 -0.80210329 0.63432226 1.52546755 0.14200823 -0.95287090 1.269227032 -0.32940645 0.770986212
gs4 -0.354767925 0.21855737 -0.54770518 0.57023369 -0.40119719 1.1654367 -0.85027787 0.05797497 -0.57666632 -0.19441172 -0.84753296 -0.201717192 -0.4443591 0.31037957 1.4397151 0.144981987 1.28913756 -0.76109926 -0.8188041253 -1.1193965 -0.34735329 0.02731708 0.47050049 0.36107874 -0.24978630 0.69621376 -0.34730205 0.335664905 -0.50390439 1.479089488
gs5 1.053567012 -0.90096227 -1.22439233 1.38286556 0.72832395 0.2446611 0.64214154 1.67034063 0.94014544 -0.56337436 0.13297430 -0.003270595 -0.4892865 1.04965180 -0.9017189 -1.422587378 0.25687151 0.34246303 -1.3100855881 -0.4117660 -0.56998370 -1.04747710 -0.59951317 0.38286581 -0.42463836 0.29869964 0.69420619 -0.224502898 0.01378260 0.259999076
gs6 -2.244409734 0.99135128 -1.25755227 -0.48107465 0.77088243 1.1587775 0.84165607 0.70800821 0.04455796 1.20866884 -0.08722013 -0.339734762 -0.3068380 -1.26475846 0.1691293 -0.016173483 0.08935879 1.04034445 -0.7302067427 0.3619944 0.09955336 -1.47161635 1.46668998 -0.57430525 -0.57827541 1.08697889 -0.36812846 -0.225673601 -0.63259981 0.540615686
gs7 0.052740026 1.67321048 1.06844511 -0.63335768 -1.29665110 -0.1715307 -1.66933194 -1.66163147 0.96745704 -1.98236849 0.39924531 0.780997272 1.5031445 0.82365265 0.7355819 -1.291690222 0.59198917 0.44201538 0.7748958150 -0.8715253 -0.42109173 0.38678646 0.62509742 -0.34088470 -0.73371942 0.45694938 -0.16347393 0.245014602 0.54802183 -0.837987628
gs8 0.128940466 -0.29023472 0.89066527 -0.61440040 -0.38274282 0.3546077 0.27907069 0.36742752 -0.96538900 -0.68424061 0.41316821 0.891427943 0.8562297 -0.82606670 0.9954917 1.271105299 -1.57441049 0.58613131 0.9237786732 -0.5526007 -1.00447106 -1.18216783 0.80591481 0.04182974 1.50238637 -2.48809418 0.67198869 0.329970369 -0.23288683 -0.512429049
gs9 -0.529924217 -0.50455633 0.14056762 0.82608534 -1.08452996 -2.4214825 -0.82702123 -1.51917889 -0.46117537 0.51536039 0.59351509 -0.477518222 -0.9141765 -0.36202472 0.2121035 -0.573687565 1.07691896 1.45448291 0.9987170368 -0.3781715 0.53631214 -0.44654865 1.24408983 0.30795693 -0.37080302 1.21990637 -0.38428269 -0.709115714 2.34614281 0.492038227
gs10 0.818321331 -1.51317539 -0.69457073 -0.49203352 0.36057893 -0.2397877 1.75081101 -0.06994105 -0.63367045 1.19094149 -0.90730458 0.767877575 -0.7928538 -0.06625141 1.5861559 0.979933067 -0.44783025 1.27989685 -0.4868701103 -1.0117896 0.94361547 1.85673623 -1.61731898 1.21625436 -0.28647246 -2.18059795 0.27744213 -1.003408010 0.30192017 -0.886608508
gs11 0.367678555 0.91252056 -0.42227266 -0.97087272 1.79158580 1.2585482 0.94342732 0.33332996 0.25752326 1.08956985 0.42462020 -0.463361537 -1.0340709 -0.62851508 -1.0342834 -1.514469249 -1.59087446 -0.08592467 0.5711694824 -0.2126554 -0.78142230 -0.16484959 -0.11708371 -0.06365675 -0.30699322 -1.78437695 -0.38348966 2.096264437 1.38197003 0.130964576
gs12 0.407633162 0.06089458 -0.03551973 -0.80557241 0.28472856 0.3839476 0.03138942 0.13026214 1.25696925 0.64914081 1.03413817 -2.014871071 -0.6371566 -1.64623803 -0.4174678 -1.889613999 0.17910813 0.02329786 -0.0009531196 1.3544298 0.64070445 -0.12299599 0.34538224 -0.04683912 0.06609172 -0.03387139 1.19121339 0.002288050 -0.67084599 0.280325902
gs13 1.117333034 1.17636696 0.90610556 -0.20339948 -1.76940395 0.6695672 1.67072725 -0.88508357 0.21042968 1.10554677 -1.20938609 -0.936796828 -0.5420542 -1.95749072 -0.1021446 -0.326335251 -1.38725541 0.03867057 1.2922253522 -0.2178358 1.11848269 0.61807105 -0.58824635 0.51758303 1.16189807 -0.11542606 0.56125057 -1.102475834 0.07801156 -0.898935092
gs14 -0.087991419 -1.48961560 -1.81093995 1.52077150 0.42263796 -0.2523003 1.81177614 -0.98653014 -0.44359835 -0.78718957 -0.27032118 0.208913565 1.4209980 1.20266088 1.0754392 -0.017917459 -0.55564302 0.04818988 -0.0639771402 0.5514408 0.12200747 -0.61335181 -2.18595402 -0.10832614 1.30303553 -0.18875480 -0.15271362 -0.366281115 -0.10674437 0.800279063
gs15 1.343950151 0.42076882 1.38439882 -0.88759686 -0.91178620 -0.4662795 -1.04143070 0.63814001 0.82957344 -0.29962403 -0.07941374 1.630590421 -0.5871337 -0.07434265 -1.5095501 1.553793983 -0.34571793 -0.82240473 -0.0947857521 0.8003060 0.21116056 0.32367880 0.86106297 1.65628788 0.97789380 -1.11080368 -1.05693195 -1.075624856 -2.14302463 -0.125154750
gs16 -2.280647404 1.45443048 -1.15615266 1.22715648 -0.91887150 -0.8774493 0.59718755 -0.53354106 -0.56650374 -0.69692215 -1.94787175 -0.263432001 1.8506749 -0.38045289 1.5196647 -0.171439192 0.23374260 0.12207975 -0.3457662199 0.8058231 -0.04857341 0.06274313 0.24285089 -0.52530011 0.36494819 0.51658411 -0.01130771 -0.356448130 1.77208671 0.310706625
gs17 -1.793915600 -0.76504524 0.63042343 0.52009464 -0.76953891 -0.6130846 2.30516686 0.87030325 1.22942353 -0.38676648 0.28786780 -1.294578572 1.0048342 0.34124188 0.6789841 -0.427903451 -0.26781132 0.36824855 0.1448156182 0.2312562 -1.65929393 1.39937404 0.85491251 -0.82632158 -1.70289841 0.74965589 -0.12891045 -0.156350687 -0.69636392 -0.127819267
gs18 1.076598555 0.66297942 0.31193924 1.21825571 -0.97634484 0.2376817 0.95228421 -0.69548369 0.64407889 -1.54705843 0.78530509 -1.141744986 1.0737459 0.20826231 -0.7801733 0.779895003 1.28313586 -0.72108935 -0.2461143875 -0.7458027 -0.38409736 -0.53680945 0.39463325 0.46243990 -0.97160166 -0.73933254 0.11490689 -0.850845941 -1.31226102 1.442617701
gs19 -0.932647493 0.36466764 -0.35976335 -0.48336730 -1.40727655 -1.7654296 -0.20079225 0.78943776 1.05075289 1.00527802 -0.38819134 0.067221765 -0.3143035 -0.09898034 -0.3791052 0.742819045 1.03125690 -0.29435736 -0.8584556405 1.5373474 -0.10243970 -0.45157605 -1.14712245 -0.58329174 0.09597807 0.98132256 0.98914383 -0.803965353 1.03267715 0.883162283
gs20 -2.507512451 -0.09179266 0.89256971 0.73127951 1.29936004 1.0227561 1.19748908 -1.12254621 0.39765236 -0.32497812 0.92840593 0.535525595 -0.6698568 -0.67309618 -2.7854267 1.470107881 -0.08598559 1.74783328 0.5261305573 0.1206040 0.50408329 0.08501165 0.83770748 0.10297851 -1.04236424 -1.27093846 -0.79581565 -0.156645031 -0.34413218 -0.528404617
gs21 1.590666101 1.21727966 -0.51796988 -0.70384659 0.47869886 0.6412920 1.08855268 -0.47402976 0.08376531 0.13287875 -0.58417864 -1.418465566 0.3586347 -0.06298446 1.0527743 -2.146897926 -0.23073419 -1.51825713 -0.0886423308 -0.8228190 -0.89776066 -0.01018669 0.03607537 -0.23848721 -0.91307940 2.16316601 0.88039149 -0.180082700 0.42559671 0.658650146
gs22 -1.314146576 0.56105707 -0.29581903 0.01879511 0.70153285 -0.4595619 0.79526977 -0.30610624 -1.59054925 -0.12272649 1.47363794 -0.919840374 0.3988845 0.50906124 -0.1078853 0.005275414 -0.80093636 0.02875750 0.1796627484 0.8606802 -0.14613823 -0.08254134 1.34492879 1.33240524 -0.72078684 -0.13081350 -1.79095355 1.829439862 -1.03960553 -0.210977661
gs23 0.007467771 0.87566015 0.10324376 0.43422509 0.89948175 1.4248760 -0.42838198 -0.63377944 -1.60531538 -0.81617333 0.71976579 0.178541229 -1.5026766 1.31351070 0.5908263 0.295870288 0.31272798 0.41614095 1.5239090790 -1.0149427 0.50905084 0.08055801 -2.05892070 -1.43447026 0.75255573 1.23995792 -0.53070949 -0.671543192 -0.97238791 -0.009068384
gs24 0.962632242 0.95541708 -0.19066384 -0.23175174 -0.76110030 -1.4063679 -0.89610030 0.66372973 -0.80965792 0.08779694 1.43555471 -0.290334626 0.2202661 -0.20314804 -1.7974438 1.986615879 0.30858557 -0.81071709 -2.1361827974 0.5564193 1.76375887 -1.03057351 1.32045107 -0.52316315 0.55080127 0.67747310 -0.41157504 -0.004477188 -0.66154101 0.675296303
gs25 0.750300473 -0.69054276 1.18919625 0.22555676 -0.89812453 -1.9043047 -0.08872006 -0.53073008 -0.25382802 0.61889062 0.54487413 0.150650635 -1.1560727 0.67452679 -0.4169377 0.301273856 0.27364471 2.12016724 0.2984327507 -0.7254619 1.57708274 -2.55299380 2.35308624 0.03326361 -1.15647532 -0.70205328 1.05030170 0.062511954 0.46103929 -1.608554943
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> canonicalC2BroadSets <- c2BroadSets[c(grep("^KEGG", names(c2BroadSets)),
+ grep("^REACTOME", names(c2BroadSets)),
+ grep("^BIOCARTA", names(c2BroadSets)))]
> MSY <- GeneSet(msYgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="MSY")
> XiE <- GeneSet(XiEgenesEntrez, geneIdType=EntrezIdentifier(),
+ collectionType=BroadCollection(category="c2"),
+ setName="XiE")
> canonicalC2BroadSets <- GeneSetCollection(c(canonicalC2BroadSets, MSY, XiE))
> huangPar <- zscoreParam(huangArrayRMAnoBatchCommon_eset, canonicalC2BroadSets,
+ minSize=5, maxSize=500)
> esmicro <- gsva(huangPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esmicro)[seq.int(min(nRowsToPrint, nrow(esmicro))),]
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.08200762 -3.52041732 -3.26174022 0.51755585 4.3317957 0.20731183 0.79679064 0.79926124 0.8990293 -0.3162241 1.37146559 1.28865093 0.08780809 -0.04487147 -0.91082622 -2.01743735 -3.12498579 -2.43416998 1.66792540 0.63671241 0.98429879 -2.77176425 -2.57368171 1.08251788 1.86537795 -0.2611243 0.3413125 -0.86055908 -1.49156413 1.32126944 2.69602243 1.710794035 0.8409827 -1.34346099 1.04123139 0.362705265
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.22642469 2.71693263 -0.10717960 -2.55590909 1.8299224 -0.47957924 -0.54472874 -0.02445334 0.9176705 -2.7381498 2.48189970 0.83060592 0.38079534 3.38221199 -0.32877740 -2.83603934 -4.22277480 0.30241154 1.04250419 1.46120065 -2.03473559 -1.21891964 1.08436248 1.06426425 -1.55401694 -0.5226624 -1.2189195 -0.45981366 -1.44418236 -0.97635055 0.50837155 0.687584202 2.5479218 0.26221667 2.58838008 -1.048488516
KEGG_PENTOSE_PHOSPHATE_PATHWAY 1.36770713 -2.36222774 0.04423311 0.12728501 4.5866555 0.73826068 -0.30430005 1.12280301 0.7386334 -0.4741849 1.94803182 0.77746818 -0.21649571 1.53618820 -1.14034304 -2.06467802 -3.35703927 -0.52856032 1.23074711 -0.38012652 1.09162981 -1.97458243 -1.97155134 0.40676902 -0.11013586 -0.8840621 -0.1723332 -0.55469059 -1.82128559 -0.27395469 0.21881375 1.100739928 0.2091012 -0.73264959 1.63276978 0.445364274
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.24894806 1.15822465 -0.63403859 -2.85893527 -0.1383472 -0.23236162 -0.85909142 0.52113731 0.4042918 -1.2811704 1.65377601 1.05051126 -1.44312727 1.72029902 0.59548843 -1.29956124 0.13453374 1.14525277 1.29207698 0.58036810 0.53523531 -0.44979114 -0.57051676 -0.15789451 -0.25900848 -2.1421868 0.4292179 1.66346748 -0.71371117 -0.01810125 0.12724512 -0.774738588 0.2843053 -0.03222607 0.34212600 -0.021697443
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.09155076 -1.97525177 -1.45276746 -0.07481523 3.5602457 0.21410187 -0.46891224 0.48276577 0.8301800 0.2782034 1.76137958 -0.30167366 -0.36866461 1.40519024 -0.46806431 -1.89929335 -2.77414056 -1.44200425 0.06351456 0.43244830 0.47487440 -0.05968271 -2.47979046 0.88521908 1.45849373 1.4370859 0.7227373 -2.42689891 -2.32001921 -0.69902703 1.80940353 1.445144270 1.1884455 0.36808537 0.73860677 -0.436670241
KEGG_GALACTOSE_METABOLISM -1.50220635 -2.12210786 -2.26086463 0.19222532 3.7806514 -0.02135668 -0.06191917 0.04740533 0.3036345 0.8632324 0.86542561 0.79337892 0.94383717 0.64846184 -1.52736862 -2.10108047 -2.57431539 -2.81169968 1.46044938 1.54579783 2.08963590 -1.37567056 -3.06980601 1.26834691 2.35203893 -1.1214375 2.0145262 -0.70745876 -3.08391089 -0.38893891 1.12194963 1.625915928 -0.1365118 -0.66174770 1.84065605 1.770831772
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 1.62312696 -0.15873213 0.21618956 0.46858637 0.9166095 -1.04599221 -0.27045669 1.11594251 -0.7483182 -0.1238161 -0.08764850 -0.32826008 0.34447096 1.24438098 0.61296527 0.15432850 0.45526120 -0.36519590 0.20463352 0.04105416 -3.40788046 -0.10615080 0.03162673 0.30778305 0.76679284 0.7047822 -2.6927801 -0.49668598 -0.74070175 -0.19230287 0.78253260 0.019056184 1.1861060 0.56044201 -0.99809984 0.006350524
KEGG_FATTY_ACID_METABOLISM 1.35637843 1.25200293 1.07298339 -1.71740038 2.3901222 -0.36157315 -0.61828083 2.30667544 1.7661146 -1.3820937 1.13392622 0.56871041 -0.79388010 1.09003603 -0.36094837 -2.90971040 -1.94439447 -0.01160654 1.33989630 0.15215352 -2.89938246 0.22556399 -0.77232732 0.57215286 -1.83412952 -0.7752354 -4.1289987 0.02530249 -0.63474809 -0.08583303 1.30223207 0.651511781 4.0322588 0.16603308 0.29172425 -0.465236301
KEGG_STEROID_BIOSYNTHESIS 1.36553599 -0.12013577 -3.08293491 -1.34327805 1.3358376 -1.11364214 1.86689706 1.85283136 1.5670901 -1.7482283 0.54388973 0.03810215 -1.44328919 1.85735478 2.10172330 -2.62881691 -2.32801957 1.24532010 -1.02033468 0.69913015 -0.29822576 -1.97008651 -0.19118335 0.33269001 1.52165526 -2.1837464 -2.2547570 -1.83792686 0.06447423 2.18187799 0.88568269 1.120120992 1.0123686 1.94734636 0.53060126 -0.505924347
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS -0.08350356 0.59893449 -0.18051314 1.46849025 -0.5398104 -0.94926659 1.14314746 0.90284639 -0.9560743 -1.7658533 -0.74679073 0.45581317 -0.76088516 0.75908154 -0.92291196 -0.68856752 -1.36785514 0.55938543 -1.85379029 0.65684292 -1.41481016 0.37705982 0.35137739 1.54211015 -0.08423593 -0.8595118 -1.1072458 1.75411782 0.91579317 1.05847124 1.52536833 -0.703220257 0.4891219 0.94531073 -0.02348034 -0.494945723
KEGG_STEROID_HORMONE_BIOSYNTHESIS 2.15700695 0.10244885 -1.53755271 0.84766905 0.5856113 -2.09650629 0.33261928 0.53843117 -0.6734007 -0.4685420 0.95573879 -0.82998047 -1.41476255 0.62639471 -0.09031677 -0.08950504 0.11011468 -0.44476912 -0.28512821 0.29866023 -1.98900643 -0.24411969 -1.43499147 0.86760041 1.02524276 -0.5932665 0.1374354 0.21201533 0.34436727 -0.41016807 2.07943956 0.425593065 0.3466719 1.06122025 -0.79768577 0.345420779
KEGG_OXIDATIVE_PHOSPHORYLATION -4.63240554 6.67049017 3.29453045 -5.55357439 0.5496431 1.77914583 -1.36568735 -0.24226839 -0.9307871 -1.1747541 4.67610019 -0.89434533 0.91778294 3.85769951 -0.94501694 -4.63557269 -3.61619441 2.54955115 3.68603811 -2.72776413 -3.86124115 -1.43398278 -0.68050376 3.04817148 -2.44714051 2.1306825 -0.6471011 -2.51904678 -2.43888735 -1.23953015 0.48985662 0.954496754 3.8663223 1.61356139 4.95225010 -3.050518657
KEGG_PURINE_METABOLISM 0.62601378 0.18764292 1.73576348 -0.39598650 2.8634149 1.74410636 0.80345344 0.21606301 -1.3228291 -1.6357118 3.37382979 0.50309725 -1.50193862 2.70460008 0.64046292 -2.91457181 -3.24668292 1.31429488 1.82156620 -1.17862270 0.22910565 -1.92894788 -2.19958482 0.95864285 -1.79749826 0.3013226 -2.0561912 -0.90114440 -1.30231555 -0.50822552 1.03537654 -0.062022288 2.3525705 0.47295983 1.48590730 -2.417920862
KEGG_PYRIMIDINE_METABOLISM 0.68740186 0.09101204 2.69635278 -0.42133976 0.8010248 1.80959049 0.21392008 1.07077719 -1.3103447 -1.9575492 3.30744108 1.47682356 -1.85296082 2.34519272 0.79412795 -2.39568143 -2.29502648 1.96378220 1.42298942 -0.45658368 0.59630261 -2.36440463 -0.67804226 0.66537108 -2.65018728 1.2139181 -2.3138877 -2.68945636 -1.24989873 -1.77690179 0.01581421 0.070503916 4.5215289 1.03102830 0.50944514 -2.892083563
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.40749755 -0.34200633 -0.67837708 -1.23839426 0.6450508 -0.87406128 0.89718094 0.88623623 -0.5901204 -1.4540001 -0.87199772 0.42565207 -1.02900922 1.09092642 0.83055385 0.95392316 -1.75399991 -0.70209561 2.56557133 0.74972926 -1.57575278 0.32540715 -1.39589409 0.64504509 1.67331106 -0.4742681 -0.4768781 0.84809297 -0.83978189 0.95527769 1.45671942 0.108438034 -1.0078854 0.58026404 -0.78212513 0.041770444
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 1.34480378 -3.30503462 -1.85282519 0.51114612 2.0581490 -0.56269049 1.33006959 0.04421460 1.1318004 0.3368706 0.50287384 -1.78230487 -0.50480571 0.94601805 1.04369734 1.71347618 -1.44995911 -2.43340216 -2.31170012 1.06556022 0.05794706 0.22204354 -0.97366673 0.37411217 1.72881970 0.3048721 -0.3882133 -1.42262378 -0.42158817 0.60165076 0.74800845 1.017367318 -1.4705719 0.31352222 1.51764940 -0.035286398
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 3.05533939 -0.89909141 0.10954792 0.57235547 0.4626350 0.43289545 0.80738496 0.82828340 0.3856202 -1.2192401 1.88574795 0.99850668 -1.58048436 1.26624831 1.63212252 -0.17105083 -2.04406219 -0.17476728 1.10667030 -1.31693777 0.48580641 -1.58414785 0.05762645 -0.83033135 -0.25313737 -2.7494190 -3.0328378 1.09278033 0.12945747 0.94310449 -0.20656930 -0.008758587 -0.5489564 0.03192254 1.53794235 -1.202205950
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 1.99685230 3.32822203 0.58345875 -4.52030235 0.3557779 1.04571821 -0.47089329 1.67689058 2.4018633 -4.7953730 4.07552302 0.75879243 0.62123432 1.51829109 0.78422115 -1.84905687 -1.97911844 -1.19127707 1.91957992 2.24311755 -2.31132941 -1.32123330 -1.89841999 0.56302584 -1.87052188 -2.8145421 -5.7964707 2.02162198 0.16550354 1.15166897 0.62682088 -0.514715091 2.6508192 -2.05463411 2.71049379 0.188390686
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 1.21309346 1.03875454 -1.40361861 -2.52868933 0.4749534 0.80310065 -0.98833939 -0.71560160 0.3172929 -2.7148765 2.17790950 0.73901374 0.25849033 1.55020704 1.20997178 -0.08496525 -0.53778049 -0.39412463 0.91390937 1.51429190 0.98942311 -0.15970919 -0.70389239 0.07882245 0.51719734 -1.0064894 -0.3389961 -0.74168366 -1.24385664 -1.12735156 0.43249880 -1.443631927 -1.1247770 0.97292321 2.74297956 -0.686449461
KEGG_LYSINE_DEGRADATION 1.27862971 0.71944399 1.63186710 -0.15625854 1.1239366 1.48957540 -0.71067310 1.03036572 1.0590009 -1.3259578 1.96846254 0.83164708 1.37283618 -0.32318559 0.82246557 -1.99572277 -1.13322958 -0.74814377 0.55359396 1.33240395 -0.03241343 -1.11966697 -0.40789253 -0.99695879 -0.31423848 0.5315305 -3.3596078 0.11542448 -1.01289512 -0.45023277 -0.42490054 -0.226806423 0.8458865 -1.67164998 0.99545026 -1.292086374
KEGG_ARGININE_AND_PROLINE_METABOLISM -0.15234479 0.69098240 -0.76904212 -0.91208540 2.2065375 -1.38716533 1.98078525 0.27213689 -1.1158975 -0.9181385 -0.25718855 -1.95804902 -1.12474003 1.25322167 0.53928573 -0.73049153 -2.14409282 -2.25112459 1.25901808 -0.05875601 -0.95521014 0.40928361 -2.08064840 1.77638819 3.15870419 0.6818472 -0.8337812 -1.63164697 -0.97781157 1.68806097 1.53083443 1.557264638 0.1741774 1.04524198 0.46754689 -0.433102466
KEGG_HISTIDINE_METABOLISM 2.68245243 1.47002186 -0.21440898 -0.53405078 2.0496709 -0.61763413 -0.26832178 -0.37983061 -0.5973106 -1.0657640 -0.90612550 -0.21298139 -1.00379460 0.17915007 0.94116346 0.18701698 -0.07179808 0.76376118 0.27104980 -0.74947548 -0.51319501 1.37082775 -0.09200211 -0.40229269 1.15117499 -1.9075314 -2.5648368 1.27744182 -1.25796002 1.29042314 0.68066731 -1.188354315 1.0593628 0.41174254 0.03668128 -1.274939998
KEGG_TYROSINE_METABOLISM 1.91319390 0.74537191 -0.21049549 -1.42486425 0.5137825 -0.64566994 1.25615471 -0.66586315 -1.0869967 -0.7914632 0.10529750 -2.04374233 -1.41200636 2.03136776 2.15096014 -0.71526488 -0.41213522 1.77566582 -0.93917591 -1.12144350 1.31645784 0.85531594 0.03889139 -0.64170442 0.13590477 -1.9150054 -0.9753372 0.62223967 -0.54517272 -0.39983433 1.31049742 -1.405758842 0.7396993 2.28797364 0.70968153 -1.156521954
KEGG_PHENYLALANINE_METABOLISM 1.71871162 0.85028780 -1.30449583 0.02082110 0.4768936 -1.66932255 1.68462411 -0.37651941 -2.3786373 0.7308768 -0.47484731 -1.97769588 -1.05075764 0.71056611 1.08003616 -0.61325382 -1.15603061 1.11546195 0.64651489 0.26703259 0.95952300 -0.67322170 1.09967677 0.27680080 1.06176322 -1.2410279 -0.2930592 0.65188967 -0.04065992 -0.62699333 -0.09001084 -0.001369905 -0.7343008 1.97832734 0.54187752 -1.169481219
KEGG_TRYPTOPHAN_METABOLISM 1.16300387 1.44923733 0.64807218 -0.54150723 1.8798625 -1.75904518 0.40200001 1.19892690 0.7528380 -0.8030061 -0.00259142 -0.37058216 -0.79497393 1.00982067 -1.00764660 -1.04581411 -0.91849620 -0.59010610 1.71370618 0.38679017 -2.82420827 -0.14129154 -0.09195268 -0.23903564 0.93135542 0.4710853 -2.9961143 0.43059167 -1.18463698 -0.21792140 0.89276830 0.137376030 2.7846734 0.56166925 -0.53510897 -0.749738309
> pickrellPar <- zscoreParam(pickrellCountsArgonneCQNcommon_eset,
+ canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(esrnaseq[seq.int(min(nRowsToPrint, nrow(esrnaseq))),])
NA19099 NA18523 NA19144 NA19137 NA18861 NA19116 NA19130 NA19131 NA19119 NA19152 NA19153 NA19140 NA19138 NA18522 NA19192 NA19193 NA19239 NA19238 NA19210 NA19201 NA19172 NA18870 NA18858 NA18852 NA19159 NA18855 NA19204 NA18501 NA19127 NA19098 NA19093 NA18856 NA18912 NA18517 NA18502 NA19171
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 3.613776 -4.9679841 -0.49159131 1.17771731 2.7476858 0.9906586 7.8351036 2.3879352 -12.247507 5.1072799 -1.7088887 0.63969178 -0.43172043 4.310571 -1.08484087 -5.547877 1.76164051 -0.8898460 1.5516740 0.18384396 5.802682 -3.7757111 -0.84888911 -4.0044153 -2.8284060 -4.082546 3.4904554 -8.250833 -1.84490573 1.28570738 11.673596 -4.2948444 -3.9836382 5.0572394 0.389111698 1.27807521
KEGG_CITRATE_CYCLE_TCA_CYCLE 3.477784 -4.3258387 0.10679683 1.15022124 2.7107418 2.7378566 6.9986362 2.9781870 -12.336655 3.6489484 -1.0391481 -0.52824121 0.65826573 2.792346 0.29220725 -6.488304 0.72250541 -1.4678365 1.2401595 0.68473909 6.985360 -3.7270434 -0.23551620 -4.2369070 -1.5168679 -3.622173 5.4307235 -7.795052 -2.44363904 0.63072187 6.965976 -3.1341445 -4.1118426 6.2243145 1.240638472 -0.66792044
KEGG_PENTOSE_PHOSPHATE_PATHWAY 3.339370 -4.0330816 0.51583498 1.40649749 2.3302549 2.0374336 6.8119003 2.4065127 -10.353614 3.3243129 -1.0295482 1.11054456 0.15015971 3.222526 -0.22754631 -5.181391 1.31417726 -0.2722243 0.6939848 -0.36386838 4.818728 -3.5438041 -0.36599427 -3.3620882 -2.3822479 -2.812857 2.8927987 -6.781842 -1.39440389 0.65166045 6.613795 -3.4344536 -4.0261038 5.4529813 0.015849046 0.45574590
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 1.344052 -2.2158240 -0.21175907 -0.53842579 0.7156543 1.5288896 2.5831229 0.9317288 -5.466600 2.2964636 -0.8651491 -0.50386448 -0.91065031 2.898462 0.03623637 -3.073694 0.20949331 -0.2369633 1.4088917 0.05340645 6.570503 -2.3938190 -1.06915911 -2.4866369 -1.0079189 -2.759769 1.9916084 -3.275961 -0.49396629 0.49476943 5.002457 -1.8388175 -1.2006148 2.8157552 0.127652664 -0.45955629
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 2.631917 -3.4339405 0.76408579 1.94446913 0.3597460 2.0623149 5.8373764 2.2457127 -11.233068 4.4543105 -0.8609952 -0.10889232 0.29460916 2.556143 0.11638893 -4.873598 0.98963304 -0.2427547 -0.0727344 0.05007844 5.596166 -3.1119692 -0.66278612 -3.4164707 -2.3915290 -2.741625 3.6366017 -8.051503 -2.16851806 0.18545576 9.295116 -2.9409623 -4.3732252 6.2960637 0.230435983 1.13794800
KEGG_GALACTOSE_METABOLISM 1.982906 -3.9655472 0.61138910 1.15467260 1.6497432 0.8209315 5.2419040 2.1089802 -9.470991 3.7134731 -0.5181230 0.27522867 0.47877266 2.465661 0.52640555 -4.480509 1.01519660 -1.0516291 0.7645887 0.11440946 4.035460 -2.7583348 -1.29899318 -3.1760242 -0.7767365 -1.936233 2.8326448 -6.897092 -1.60000462 0.14907466 8.487595 -3.6464832 -3.5973961 5.0170353 0.116352490 1.61167165
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 2.062532 -1.7226116 0.04676367 0.09733945 1.3732660 0.6312735 3.1964202 1.1698729 -4.661225 3.5280417 -1.0282684 -0.24234280 -0.15789395 3.398797 -0.27367316 -2.285976 0.59113894 0.1038181 1.7998289 -0.70562100 1.466847 -1.9910010 -0.43593836 -1.5128138 -0.6582237 -2.253523 0.1210538 -2.828518 -1.52381952 0.63908058 3.312295 -0.9165812 -1.5677085 1.2962335 0.006141184 -0.07500485
KEGG_FATTY_ACID_METABOLISM 3.386727 -4.2988297 0.06235647 0.58211164 3.3131963 3.0678691 7.0037479 3.2012797 -11.277464 4.2927549 -1.4335746 -0.45941305 0.29576869 5.354193 0.02688667 -5.924900 1.13628254 -1.0545026 0.3870266 -0.12197680 6.536312 -3.4052486 -0.74006237 -3.1208879 -3.6370863 -4.832566 2.5697139 -7.724517 -2.04579965 1.96532286 8.388591 -2.7458801 -4.0057123 4.2475503 0.401532299 0.60919695
KEGG_STEROID_BIOSYNTHESIS 3.656540 -2.2721186 -1.57781964 -0.72604499 2.6915557 2.7253367 3.4859428 2.1396122 -7.766563 0.3563763 -1.7757330 -1.54337991 0.07930328 1.934096 -0.40859022 -3.366802 -0.91869676 -1.4728893 0.1800936 -0.22016331 4.432150 -2.6588099 0.96699753 -3.0431456 0.2835885 -1.981831 1.9816759 -5.436519 -1.29757797 0.75871060 6.245049 -1.8776229 -1.5097635 5.8384179 3.033017936 -0.93439173
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 1.116348 -0.9463790 -0.45604407 1.85063315 0.8106916 -0.3276203 1.2722726 1.5051284 -3.911297 0.4279352 -1.1991834 0.27030319 0.37304589 1.394388 -0.30774860 -1.744298 -0.92604666 -0.4823653 0.6953440 0.31728853 3.213363 -1.1520835 -0.44496503 -0.7902377 -0.8179018 -1.481037 0.8903110 -2.713066 0.11460137 0.99717578 3.970424 -0.9784062 -1.0879326 0.8027559 0.375701324 -0.63109969
KEGG_STEROID_HORMONE_BIOSYNTHESIS 2.480574 -2.2365775 -0.76345941 1.00478856 0.6737178 0.9885282 1.2763885 1.3246518 -5.234984 2.4601178 -1.4631961 -0.46795704 -0.10691565 1.885405 -0.83051072 -1.461525 -0.76902369 -1.9770725 1.6275719 -0.31312275 3.542358 -1.2925407 -1.34198406 -1.8121874 0.4845320 -1.476588 1.6850644 -3.134337 0.07214458 0.57869417 5.589447 -0.1789734 -1.8021160 1.3544518 0.029050681 -0.39441569
KEGG_OXIDATIVE_PHOSPHORYLATION 4.599553 -6.7100059 0.42751863 1.23309432 3.6403868 7.3503379 11.9441178 4.5820577 -22.111947 6.7108308 -2.6602605 -0.07351686 0.54111443 5.562369 -0.51723640 -6.354949 -0.32498263 -2.1480812 2.6116772 0.93083606 13.369164 -6.1648449 -1.26630351 -8.0783946 -5.1518001 -6.967977 5.0669407 -14.885391 1.28479521 1.01972315 14.812577 -5.0108056 -4.7390139 10.5574156 -1.074527837 -2.00447078
KEGG_PURINE_METABOLISM 6.220789 -7.3332881 2.16396498 2.57568871 3.9859659 5.9240050 10.3558058 5.7052135 -22.077635 6.8238021 -3.0415523 -0.54372207 -1.11552134 6.029539 -0.46629110 -7.154343 0.67053421 -2.8913745 4.9291899 0.29117744 13.403968 -7.1225909 -2.44539633 -8.3994983 -2.7797096 -6.288009 7.2046295 -14.113059 -0.82453646 2.33187623 12.429260 -5.8244919 -6.9103465 9.8373238 0.195600901 -1.74696832
KEGG_PYRIMIDINE_METABOLISM 6.251783 -7.3004492 2.45514238 3.55758788 3.5294787 6.1695147 10.5996032 5.4341495 -20.035750 6.8378927 -2.6453473 -0.25241143 -1.71619115 6.033213 -0.02466917 -7.150940 0.78178056 -2.2034922 2.5335758 0.25118554 10.327172 -6.6221964 -1.55381413 -7.3268938 -4.5723746 -5.782497 6.6734213 -12.451852 -0.73080869 2.09920973 9.852821 -4.1746574 -6.4184518 10.0207656 -1.585732321 -0.85976870
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 2.224928 -2.5175231 0.31954322 -0.05577043 3.0724152 2.4451896 2.5921602 2.1124348 -8.210483 2.8724531 -2.1070978 -1.60741186 -0.68246497 2.199909 -0.19364540 -3.650181 -0.42907746 -1.8261277 3.0553026 0.60745873 8.136535 -2.2790936 -1.58939303 -3.1084949 -1.7070042 -2.761089 3.4866388 -5.033765 -1.82076593 1.96304371 5.189870 -1.6042160 -2.6184510 2.5338460 1.312164296 -0.32183720
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 2.999856 -3.4375039 0.89916682 0.63033836 2.4687629 1.9603347 1.1901481 1.6342611 -6.972969 3.0118818 -2.0881152 -0.72779749 -1.62320621 3.334605 -0.62335248 -2.686378 -0.91324037 -2.4721889 2.3887953 0.02658081 6.061305 -2.0460961 -1.20709007 -2.7982678 1.6860733 -2.621328 2.2711386 -5.897327 -1.23629767 3.63007666 3.537552 -2.4197078 -2.4758398 2.1078716 2.260659728 0.14729905
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 4.528253 -4.1049604 0.95473848 2.35554742 2.7822856 2.4088547 4.0580919 3.0774039 -9.706246 4.2374134 -2.1616616 -1.01364410 -0.94299011 4.890240 0.03792379 -4.658464 0.24416843 -1.9253826 1.9851437 -0.79513338 5.959851 -3.1596842 -1.27828378 -4.1484755 -0.6797800 -3.179783 2.6697157 -6.646975 -1.44841945 2.43818842 4.976755 -2.7140771 -3.0367858 3.6516496 0.249454763 0.09506715
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 3.578068 -5.2126760 -0.06582990 1.05028056 3.1175359 2.9255891 8.6648883 2.3315356 -13.262600 4.3087913 -0.4353979 -0.65613429 0.66965563 6.611628 -0.05894749 -6.337658 0.72653584 -0.9627796 1.2156060 0.23131911 7.440367 -4.5184377 -1.26578230 -3.5938565 -3.1877200 -4.678520 3.2011377 -8.745689 -2.57894300 1.66411861 9.113690 -3.2824421 -3.9956024 4.9755314 0.821735158 0.19100324
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 2.540325 -2.5580006 -1.05293097 0.95062670 2.7166826 2.4195780 2.5974731 1.1984907 -6.563815 1.1393911 -0.6535133 -0.53905503 -0.48018704 2.677603 -0.01257593 -2.979565 -0.07920138 -1.4780887 0.6527642 0.82805025 4.578221 -2.3827049 -1.46480651 -2.3355377 -0.5622099 -2.138416 3.8006165 -4.314880 -0.76030110 1.13881051 4.554075 -2.4839790 -2.0330791 2.0076049 0.891015248 0.18152038
KEGG_LYSINE_DEGRADATION 3.602131 -5.1825796 2.10404410 1.03465213 2.2325113 3.8859631 6.2068738 3.2557411 -13.475952 4.4676256 -1.5475372 -0.64332512 0.30278276 3.096102 0.80316244 -4.861363 -0.16047923 -2.7961166 3.1711096 0.15946804 7.862459 -3.9302227 -0.46045256 -4.2726251 -0.8764999 -3.201900 3.8283383 -9.229505 -1.76236481 0.80665042 7.238060 -3.3994653 -5.0360166 5.6878045 1.220045863 -0.12912036
KEGG_ARGININE_AND_PROLINE_METABOLISM 3.552908 -2.6014549 0.25403717 0.44467074 2.9611366 2.7482330 5.2593925 2.8596838 -11.003736 4.4014280 -1.4301706 -1.48503133 -0.53070060 4.554944 -0.84220810 -4.833547 0.25503808 -1.8556128 2.1043602 0.08116681 7.166741 -2.6433864 -1.27027071 -3.8686066 -2.0615804 -3.311451 3.5978009 -7.755397 -2.32827010 2.16085780 7.856669 -2.3568083 -4.1579194 4.1342672 0.563638193 -0.62082177
KEGG_HISTIDINE_METABOLISM 2.377756 -1.5661914 0.96968517 0.67672158 0.9721192 2.3359869 3.2557159 1.0090144 -7.185205 3.1549802 -1.8899941 -0.60468775 -1.07159899 2.157091 -0.57746861 -2.782320 0.04684621 -1.1830784 1.5261956 0.19975447 3.864136 -1.8653606 0.09025289 -2.5738520 -0.6662499 -2.626624 0.5408687 -4.116989 -0.76704574 0.94226265 5.226687 -1.5137978 -1.9567396 3.5069890 0.784552904 -0.69041273
KEGG_TYROSINE_METABOLISM 1.678686 -2.8624559 0.11380858 0.96294524 0.6770510 2.7615384 3.4725219 2.3537463 -8.530014 3.5068974 -1.7874306 -0.61405904 -1.40109143 1.614691 -0.66315954 -2.873058 0.36251656 -0.9941132 1.1490792 0.76083067 7.367480 -2.0494605 -1.01357494 -2.6154799 -1.7935798 -2.941109 2.5428844 -5.886190 0.22349847 0.56447214 5.669252 -2.2344264 -1.0213345 3.1941475 0.652568301 -0.34807790
KEGG_PHENYLALANINE_METABOLISM 2.090906 -0.6398089 -0.96814219 0.10793026 0.9964645 0.5346435 0.6255186 1.3708515 -4.156439 0.9251142 -1.8077444 -0.76133326 -1.10126175 0.105535 -0.33588778 -1.258697 -0.35343074 -0.9379906 2.7207387 0.00165670 6.070485 -0.5640568 0.14502636 -1.1017496 -0.7081219 -1.161937 1.3090258 -2.597788 -0.49159141 0.02963533 1.589456 -0.9849399 -0.2852917 2.7296313 -0.251299048 -0.88510761
KEGG_TRYPTOPHAN_METABOLISM 2.427252 -1.8565270 -0.36746740 0.32340813 2.1446252 1.8352479 4.3807816 2.0802495 -8.862574 3.1187773 -1.1165949 -0.32613518 -0.01228540 3.252853 -0.62866265 -3.014655 -0.48220328 -1.8893938 2.7605496 -0.83247782 5.133392 -2.3976572 -0.27716429 -3.1951290 -0.5176048 -2.990382 1.8257622 -5.044709 -1.80260786 0.91193140 5.959211 -1.2696260 -2.5846251 3.4311657 0.932687520 -1.04941279
>
> gbmPar <- zscoreParam(gbm_eset, brainTxDbSets)
> gbm_es <- gsva(gbmPar, verbose=FALSE)
> exprs(gbm_es)[seq.int(min(nRowsToPrint, nrow(gbm_es))),]
TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 TCGA.02.0011.01B.01 TCGA.02.0014.01A.01 TCGA.02.0024.01B.01 TCGA.02.0026.01B.01 TCGA.02.0028.01A.01 TCGA.02.0046.01A.01 TCGA.02.0047.01A.01 TCGA.02.0048.01A.01 TCGA.02.0060.01A.01 TCGA.02.0069.01A.01 TCGA.02.0074.01A.01 TCGA.02.0080.01A.01 TCGA.02.0084.01A.03 TCGA.02.0087.01A.01 TCGA.02.0104.01A.01 TCGA.02.0114.01A.01 TCGA.02.0281.01A.01 TCGA.02.0321.01A.01 TCGA.02.0325.01A.01 TCGA.02.0338.01A.01 TCGA.02.0339.01A.01 TCGA.02.0432.01A.02 TCGA.02.0439.01A.01 TCGA.02.0440.01A.01 TCGA.02.0446.01A.01 TCGA.06.0128.01A.01 TCGA.06.0129.01A.01 TCGA.06.0146.01A.01 TCGA.06.0156.01A.01 TCGA.06.0166.01A.01 TCGA.06.0174.01A.01 TCGA.06.0177.01A.01 TCGA.06.0238.01A.02 TCGA.06.0241.01A.02 TCGA.06.0410.01A.01 TCGA.06.0413.01A.01 TCGA.06.0414.01A.01 TCGA.06.0646.01A.01 TCGA.06.0648.01A.01 TCGA.08.0245.01A.01 TCGA.08.0344.01A.01 TCGA.08.0347.01A.01 TCGA.08.0348.01A.01 TCGA.08.0350.01A.01 TCGA.08.0353.01A.01 TCGA.08.0359.01A.01 TCGA.08.0385.01A.01 TCGA.08.0517.01A.01
astrocytic_up -0.08909934 -3.152221 0.8107079 -5.2069957 -1.033834 -3.508842 -3.1829696 -0.6973523 2.015886 1.1632330 0.8404895 -2.159491 -2.548436 -0.8250184 -3.4106404 -4.002532 -4.613817 -3.044947 -5.242683 -1.2277799 -2.5902555 -3.9951172 -5.281595 -0.1906933 1.3229285 -2.3332362 2.2376210 -1.582096 -3.701165 -1.7871696 0.1453581 1.3152286 -0.9330403 -3.939937 -3.847457 -2.256774 -3.6583197 -3.343534 -1.732189 -0.3798295 -3.595637 -2.2691422 -3.4280276 -0.6868929 -1.5292866 -3.6440129 -0.8287959 0.4759527 -3.1435814 0.6136584
astroglia_up -3.10555037 -7.101899 -4.0708334 -9.6701263 -3.664210 -5.299715 -6.9344991 -2.4056788 2.838336 -4.0490130 -3.1252581 -3.831245 -2.365279 -7.0701428 -1.7311405 -3.642857 -9.353379 -6.868324 -6.498363 2.5117857 -1.8454742 -8.1922252 -8.284021 -8.5971607 -0.8126084 -2.3739610 0.8329655 -4.621603 -7.722374 -6.1625899 0.7790239 0.7748605 -2.9931959 -2.105014 -4.057559 -3.331656 -3.4418359 -4.645598 -3.835184 0.7608445 -4.037412 -3.3140937 -8.1346699 0.6228006 -1.9891070 -3.3462253 -1.0731883 -1.4644452 -5.1808878 -2.8928713
neuronal_up 7.37537036 0.902553 0.3057596 0.2300378 6.512670 -1.073758 -3.5261610 3.0524882 3.747227 0.1086332 7.3042698 -5.441629 -4.460294 -4.1315377 -0.9454844 -3.971821 3.422017 -4.541850 -2.411690 0.8123934 1.3326064 1.2388876 1.226472 -1.2244988 -1.4490155 0.2784605 5.5226593 -3.202053 -3.079236 -2.3312546 0.4439339 -0.4968675 2.5700910 2.587650 4.151428 -1.103735 0.1977171 3.893207 1.635213 -0.4158050 2.809088 -2.6602840 3.1488241 3.7441383 -0.2328512 -3.6994980 -3.8924016 8.6663741 -1.6945566 0.3744679
oligodendrocytic_up 3.29318629 1.254525 3.2712757 2.7191887 5.272348 1.175787 -0.2208184 3.3361411 3.463337 -0.8905276 4.5060174 4.925995 9.254130 1.6478948 -2.4138339 2.381934 -4.283642 1.802069 2.652757 0.6540577 0.6721184 -0.2149802 2.097069 1.0987993 3.9911220 3.4783625 5.9792216 1.707458 5.240817 0.4118169 2.0783070 4.4474700 2.4108206 4.348025 1.816250 5.848493 -0.1675866 3.913055 6.890191 -0.1129943 2.247621 0.3634295 -0.8202027 3.2955322 5.6991646 -0.6973273 0.6332216 0.5563794 -0.7722805 2.2257859
TCGA.08.0524.01A.01 TCGA.12.0616.01A.01 TCGA.12.0618.01A.01 TCGA.02.0089.01A.01 TCGA.02.0113.01A.01 TCGA.02.0115.01A.01 TCGA.02.0451.01A.01 TCGA.06.0132.01A.02 TCGA.06.0133.01A.02 TCGA.06.0138.01A.02 TCGA.06.0160.01A.01 TCGA.06.0162.01A.01 TCGA.06.0167.01A.01 TCGA.06.0171.01A.02 TCGA.06.0173.01A.01 TCGA.06.0179.01A.02 TCGA.06.0182.01A.01 TCGA.06.0185.01A.01 TCGA.06.0195.01B.01 TCGA.06.0208.01B.01 TCGA.06.0214.01A.02 TCGA.06.0219.01A.01 TCGA.06.0221.01A.01 TCGA.06.0237.01A.02 TCGA.06.0240.01A.02 TCGA.08.0349.01A.01 TCGA.08.0380.01A.01 TCGA.08.0386.01A.01 TCGA.08.0520.01A.01 TCGA.02.0007.01A.01 TCGA.02.0009.01A.01 TCGA.02.0016.01A.01 TCGA.02.0021.01A.01 TCGA.02.0023.01B.01 TCGA.02.0027.01A.01 TCGA.02.0038.01A.01 TCGA.02.0043.01A.01 TCGA.02.0070.01A.01 TCGA.02.0102.01A.01 TCGA.02.0260.01A.03 TCGA.02.0269.01B.01 TCGA.02.0285.01A.01 TCGA.02.0289.01A.01 TCGA.02.0290.01A.01 TCGA.02.0317.01A.01 TCGA.02.0333.01A.02 TCGA.02.0422.01A.01 TCGA.02.0430.01A.01 TCGA.06.0125.01A.01 TCGA.06.0126.01A.01
astrocytic_up -4.0501595 -3.58528280 -2.150553 2.6903341 4.4208691 8.164340 2.1478449 2.838322 2.5975997 0.37673200 2.838609 2.075690 3.310031 1.3772906 4.1679206 3.366810 1.771455 1.1231341 -0.3661421 4.8202400 1.8597821 0.2832633 -3.299052 0.4615451 2.080973 0.75936460 1.128923 1.91788210 3.565186 2.8923945 1.620005 3.9857385 2.1520939 1.5575374 1.4959032 4.756540 -2.867930 -0.6443480 0.85949798 -1.785971 -1.176208 -0.7720236 2.199689 -0.4467583 -0.06920086 -0.1063925 1.59512455 0.2113819 2.180979 1.594056
astroglia_up -7.8449103 -3.69159341 -5.755313 3.0432536 -0.4214884 3.141192 0.4343735 1.984018 -0.1593382 0.03139333 -5.837569 -1.925856 -5.373983 -0.4965235 0.8055162 1.604746 -1.688300 -0.5820614 -5.4221591 -1.9257791 1.7990137 -1.8344248 -5.126051 -2.2978494 -3.971752 -0.08022663 1.269094 -0.04203954 0.291440 1.2673922 -2.484940 -1.8906992 -0.3366926 0.1137957 1.2937214 3.049417 -1.620135 2.3199253 -0.15299389 -4.373301 -3.517849 0.7444723 1.008946 0.7440944 -1.30587497 -1.1595379 -0.12211222 -0.7345510 -1.016347 -2.525468
neuronal_up 0.7621561 -1.58714007 3.908310 5.1544726 -2.8583933 6.461310 2.4198545 13.914963 4.5975953 1.16075755 26.315151 6.131003 28.314920 0.9021609 2.6534158 10.109527 -1.392535 2.0200464 12.5550187 1.4292865 0.5672497 2.9720049 5.488963 -1.8932872 22.021493 4.08113876 1.624494 4.29047134 1.231357 1.0326487 -6.201044 3.2394715 -4.5485246 3.5140611 0.8060133 -2.388428 -5.656942 -5.3246569 -0.02576302 -2.989774 -2.180673 -2.7829681 -1.709889 -4.0113452 -5.27955635 0.1081630 -0.65506207 -5.1568867 -2.899157 1.900477
oligodendrocytic_up 3.4473515 0.08207331 2.122737 -0.4139425 -3.6839021 1.784584 1.6375784 3.111439 -1.1400225 0.24599609 2.236097 -1.539376 1.530867 1.2539415 1.4258764 3.523489 -2.181047 -2.2383685 -1.0576358 0.2384092 4.2246382 -0.1492978 -3.327585 -0.7908182 2.860221 -1.23331168 -1.455083 -1.56496385 -2.848318 -0.4789735 -1.910726 -0.6964973 -0.9156850 -3.7150977 -0.1130542 3.021765 -1.968815 -0.8635538 -2.90146119 -3.962522 -4.266302 -1.8826848 -2.813841 -3.7335868 -2.67976967 -3.3860511 -0.08389153 -1.4103498 -1.328776 -1.187159
TCGA.06.0137.01A.03 TCGA.06.0145.01A.04 TCGA.06.0148.01A.01 TCGA.06.0187.01A.01 TCGA.06.0211.01B.01 TCGA.06.0402.01A.01 TCGA.08.0246.01A.01 TCGA.08.0354.01A.01 TCGA.08.0355.01A.01 TCGA.08.0357.01A.01 TCGA.08.0358.01A.01 TCGA.08.0375.01A.01 TCGA.08.0511.01A.01 TCGA.08.0514.01A.01 TCGA.08.0518.01A.01 TCGA.08.0529.01A.02 TCGA.08.0531.01A.01 TCGA.02.0057.01A.01 TCGA.02.0004.01A.01 TCGA.02.0006.01B.01 TCGA.02.0025.01A.01 TCGA.02.0033.01A.01 TCGA.02.0034.01A.01 TCGA.02.0039.01A.01 TCGA.02.0051.01A.01 TCGA.02.0054.01A.01 TCGA.02.0055.01A.01 TCGA.02.0059.01A.01 TCGA.02.0064.01A.01 TCGA.02.0075.01A.01 TCGA.02.0079.01A.03 TCGA.02.0085.01A.01 TCGA.02.0086.01A.01 TCGA.02.0099.01A.01 TCGA.02.0106.01A.01 TCGA.02.0107.01A.01 TCGA.02.0111.01A.01 TCGA.02.0326.01A.01 TCGA.02.0337.01A.01 TCGA.06.0122.01A.01 TCGA.06.0124.01A.01 TCGA.06.0130.01A.01 TCGA.06.0139.01A.01 TCGA.06.0143.01A.01 TCGA.06.0147.01A.01 TCGA.06.0149.01A.05 TCGA.06.0152.01A.02 TCGA.06.0154.01A.02 TCGA.06.0164.01A.01 TCGA.06.0175.01A.01
astrocytic_up 2.676893 4.30587603 -0.1484128 2.121824 1.193762 0.216868 2.098520 -0.3590077 1.4924973 3.1318506 -1.885732 1.708314 2.657195 4.545553 2.912760 1.9804288 3.802850 4.534642 -0.003929236 3.2517485 -2.888534 0.1771372 -1.1738971 2.8936005 -2.743719 1.2918124 0.08247081 -1.203403 1.4767707 -0.304507 -2.321400 -0.4437532 -0.3035455 1.4292700 0.6915937 4.0222928 0.19722388 -4.5950920 -0.9341628 0.3305044 0.1631184 -2.8586504 -0.5955305 -0.2539437 0.8313484 1.589897 -0.7911376 1.293819 2.079665 0.9014619
astroglia_up -1.410315 0.04597652 2.5770285 2.311639 -3.398351 -1.272882 2.373027 1.6009710 -0.2377814 -0.0469951 -3.575104 -3.168532 2.258187 1.899525 1.815670 0.1310026 -0.363329 3.570761 8.762186646 3.2915183 6.806357 6.3444795 5.9779424 5.6455262 2.528754 3.0563019 8.59482813 2.857618 5.3890853 3.179268 3.523551 3.7860581 3.8898683 6.9126141 4.3234965 7.5338826 4.60504082 -0.2121851 4.2592086 3.3834519 4.3762196 5.9914008 5.4677275 2.1915212 6.4911546 2.848080 -0.7855700 4.469387 5.496258 2.8326382
neuronal_up 2.935035 -4.33202655 -2.3779648 -4.899466 1.924114 -2.897353 -2.767796 -3.8811350 -0.3370994 1.1164572 -4.545340 -6.060301 4.539371 -3.571778 -5.669859 -2.6699004 -3.006828 -3.455450 -1.900261556 0.6429803 -3.745943 -4.3142406 -2.7433338 2.6788158 -2.270892 -1.1439441 1.03773052 -2.029232 -6.1026313 -3.833959 0.559603 8.2443008 -2.5442885 -0.3626451 -2.5297864 -0.5810968 -2.26408321 0.6219462 -2.1951042 -3.4844647 -2.0629756 -3.2574162 -4.6249237 -4.2837280 -2.9083139 -2.304073 -4.9578554 -3.231750 -2.616099 2.6652850
oligodendrocytic_up -1.429602 -1.16836372 -3.3273872 -1.484285 -2.102452 -3.335235 -1.695018 -2.8550582 -5.1228981 -1.1518311 -4.754625 -2.497824 -1.200832 -3.091723 -2.826340 -2.3319305 -2.020322 5.901598 -1.869680552 1.5415212 -1.287606 -0.8869270 0.6441386 -0.9799234 -4.562924 -0.1648678 -2.00977500 -3.914152 -0.6328189 -1.448776 -1.641520 4.8529785 -1.1013767 -0.1757191 -1.5306714 0.6552283 0.05824521 -1.7220446 6.6503840 -0.2605514 -1.7376517 -0.6012265 1.1494110 0.9321423 3.3145489 -3.385071 -3.7834245 -2.604791 2.660582 1.3763185
TCGA.06.0176.01A.03 TCGA.06.0184.01A.01 TCGA.06.0189.01A.05 TCGA.06.0190.01A.01 TCGA.06.0194.01A.01 TCGA.06.0197.01A.02 TCGA.06.0210.01A.01 TCGA.06.0397.01A.01 TCGA.06.0409.01A.02 TCGA.06.0412.01A.01 TCGA.06.0644.01A.02 TCGA.06.0645.01A.01 TCGA.08.0346.01A.01 TCGA.08.0352.01A.01 TCGA.08.0360.01A.01 TCGA.08.0390.01A.01 TCGA.08.0392.01A.01 TCGA.08.0509.01A.01 TCGA.08.0510.01A.01 TCGA.08.0512.01A.01 TCGA.08.0522.01A.01 TCGA.12.0619.01A.01 TCGA.12.0620.01A.01
astrocytic_up -1.5182935 1.414137 0.6145721 1.3611626 0.9299387 -0.6118263 -1.9077298 -2.977643 2.354636 1.256214 -1.0446336 -0.03521543 -0.2048689 0.08255436 -0.5703374 -0.5160375 -4.393404 -0.04869947 1.0193142 1.716183 -3.050138 -2.968484 -1.4182898
astroglia_up 3.6679577 2.016040 3.8365848 5.3857249 3.6519214 4.1911267 2.2371880 2.996960 3.653019 2.850722 5.3799630 4.07607902 4.5965300 3.82064210 6.8146847 2.5472498 2.787112 3.48964654 3.3631687 7.909505 4.609892 2.788675 1.2952133
neuronal_up -3.5923614 -2.462081 -3.0230934 -2.2989952 -2.9441875 -2.8335093 -2.8902359 -2.778339 -2.445036 -4.896693 -0.7803416 0.16600660 -2.5170378 4.64377108 -4.2430666 3.5077554 -2.229394 0.68892787 -4.1220154 -2.572970 -2.437011 -4.344700 -3.5499763
oligodendrocytic_up -0.4309207 1.205395 -3.3004554 -0.2007412 -2.3954090 -2.6221966 -0.6024445 -1.075083 -2.183149 -1.983176 -0.3895268 -0.45898726 0.9638120 -1.89896706 -1.4509535 -0.1200174 -4.067190 -1.98215669 -0.5922569 -1.755122 -2.906155 -3.149109 -0.9366359
>
> cgpC2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> leukPar <- zscoreParam(leukemia_eset, cgpC2BroadSets,
+ minSize=10, maxSize=500)
> leukemia_es <- gsva(leukPar, verbose=FALSE)
Mapping identifiers between gene sets and feature names
> exprs(leukemia_es)[seq.int(min(nRowsToPrint, nrow(leukemia_es))),]
CL2001011101AA.CEL CL2001011102AA.CEL CL2001011104AA.CEL CL2001011105AA.CEL CL2001011109AA.CEL CL2001011110AA.CEL CL2001011111AA.CEL CL2001011112AA.CEL CL2001011113AA.CEL CL2001011114AA.CEL CL2001011116AA.CEL CL2001011118AA.CEL CL2001011120AA.CEL CL2001011121AA.CEL CL2001011122AA.CEL CL2001011134AA.CEL CL2001011150AA.CEL CL2001011151AA.CEL CL2001011153AA.CEL CL2001011154AA.CEL CL2001011126AA.CEL CL2001011127AA.CEL CL2001011128AA.CEL CL2001011129AA.CEL CL2001011130AA.CEL CL2001011131AA.CEL CL2001011132AA.CEL CL2001011133AA.CEL CL2001011138AA.CEL CL2001011139AA.CEL CL2001011140AA.CEL CL2001011142AA.CEL CL2001011143AA.CEL CL2001011144AA.CEL CL2001011146AA.CEL CL2001011149AA.CEL CL2001011152AA.CEL
NAKAMURA_CANCER_MICROENVIRONMENT_UP -2.3189547 0.55622710 -3.11198172 1.4986887 0.79561210 1.27047787 -0.65748275 -3.6475523 -0.938530423 -2.2124263 1.492202601 -0.73476415 1.14702413 -1.8556094 -0.10710987 0.62555189 -1.84985291 -1.99696364 -1.6391298 0.7733034 -0.76199840 -0.11481253 -1.54473797 2.90988107 1.91589932 0.306170802 1.84065500 1.0454556 -1.7550145 -0.64379309 3.1809700 1.66381825 0.85600132 1.5031001 5.27303344 -0.3741954 -2.3891628
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP -0.1437327 1.34145819 3.12030398 -0.9451609 -0.65236606 -0.75734866 2.49198413 -0.6960575 0.479216286 4.2298075 1.699907478 1.80608946 -0.55495287 -1.2596018 0.67756954 -0.22151006 -0.57450357 0.22116396 -1.9389978 -1.6951874 1.38964755 -0.02115285 -0.93820411 -0.54585990 -0.77666967 0.094771714 -0.46941562 -2.4584473 -3.2781747 -0.41248115 1.9550954 2.96291598 0.77692080 -1.1198979 1.01968846 -2.1157809 -2.6910370
WINTER_HYPOXIA_UP -2.2032116 1.94192756 -1.01905531 -0.2262124 -1.70570515 -1.31370553 -1.53784382 -4.1896689 -0.573056157 1.3188203 -1.630985843 2.11056496 3.86978019 1.7943601 -3.47417711 -0.09511845 -1.03683603 -1.41318482 -2.0541609 -2.5022841 0.95884756 1.99489650 0.01912947 -0.40707157 1.49731005 1.876664626 0.82794692 1.3034511 -1.9570481 1.23100844 4.5355537 2.45428354 2.43716611 -2.4481408 1.95214281 0.4155076 -2.7518949
PYEON_HPV_POSITIVE_TUMORS_UP 1.8425924 -0.90371747 4.42311845 -3.7133346 1.07235312 1.59420262 1.54184230 5.1765404 4.512483991 5.3940779 0.528141105 6.86588624 -5.27763956 0.5196579 2.48547689 -1.84517673 2.66475634 3.44169814 -0.7470868 -5.1281340 -0.05626604 -1.23659933 0.25586378 -3.15164039 -4.16550799 0.041309197 0.47627197 -2.3210603 0.1246063 -5.22630542 -2.5795122 3.27132937 -0.03055620 -2.0519735 -3.90153690 -3.1462161 -0.7499449
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP -2.0355786 2.60368733 1.65952935 -0.2731903 -2.82481184 -1.60635471 0.40429957 -6.5356063 1.373085999 3.2217230 -0.004117969 3.12303563 1.37715940 4.3192977 0.04425356 -1.21708631 -2.06097063 -0.94940011 -2.9791103 -4.4507436 1.15163993 -2.13360896 -2.04857971 -2.73828950 3.09070632 0.890670934 -2.19450875 1.7569005 -2.1019689 1.35470426 5.2654387 2.89066529 3.53097016 2.9110126 0.45673634 -0.7116174 -4.5599727
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP -6.1743193 2.10626458 -9.93033191 5.5020838 1.24528029 2.76706915 -0.76977556 -10.1318343 -1.226965247 -0.2985038 3.204167870 -2.06583449 4.01539216 -1.4989300 -0.80243199 -2.09676668 -3.92339728 -4.76956131 -3.5492403 0.6307940 -6.10750595 -0.36445017 -5.33447764 3.97968003 1.06375876 -1.501968354 4.59460616 3.0050082 -5.2099545 4.59692879 8.4071865 3.02679350 4.62088574 4.2776647 8.40747357 2.6954767 -2.3902658
LU_TUMOR_VASCULATURE_UP -2.3516037 0.23422156 -3.24709239 1.9002877 1.06371531 -0.31124003 0.64150436 -4.4921642 -0.429394270 -0.4708068 1.209418772 -0.53680406 -0.18120399 0.1020756 -1.17510637 -0.13495767 -1.60844266 -1.61180192 -0.2395109 1.6463378 -2.91072538 0.28004166 -1.85054840 3.12872425 0.81025980 -0.427636238 1.02779187 1.5058078 -3.8168552 3.69953701 1.2982542 1.83497935 0.73751145 2.3115023 1.90714553 1.9502801 -1.4935021
KORKOLA_EMBRYONAL_CARCINOMA_UP -2.0102420 1.77944838 0.71764392 0.7225229 -0.47650814 -2.94754400 -1.68662524 -2.7193614 -0.282629306 0.8789733 -0.663623433 2.48363943 0.58547469 0.9084250 -1.30090891 0.91028023 0.22038861 1.58879655 -1.9871067 -1.0238739 2.48127825 1.11685683 0.80172070 -0.88055998 -1.02367666 -0.170070225 -0.56110595 0.9707670 -0.6937145 -0.51027108 1.3912644 1.21188680 1.78787521 -2.5882821 0.35238902 1.0686185 -0.4521463
KORKOLA_TERATOMA_UP -0.3532193 2.17997348 0.03956106 1.3024658 1.85511030 0.23121185 -1.71392644 -2.2452103 -1.891420902 -1.2620777 -0.745760801 -1.54879367 -1.14580035 -0.4412586 0.13971105 1.04541604 -0.18902172 -0.56554466 0.0430148 0.3175348 1.08482965 0.62953613 0.19987932 1.49131527 -1.44961377 0.238083305 1.05678681 1.2490852 -0.7551186 -0.06277113 0.4286523 0.11269812 1.05268675 -1.7303152 0.59079381 1.2819498 -0.4704426
KORKOLA_YOLK_SAC_TUMOR_UP -0.1040637 2.99594415 1.31530981 -0.3081178 0.62832670 -2.42448384 -1.00992574 -1.6262212 0.163843219 2.4035673 0.155357913 2.06606337 0.24037257 0.4130723 -1.10335321 -0.70220925 0.89210405 1.60172761 -1.0474659 -0.7906492 1.09211241 1.15544503 -0.36703662 -0.60395345 -2.57074459 -0.583146941 -0.73629462 0.3110249 -1.7065781 -1.25258365 0.9935598 0.79136836 1.51933857 -2.7892840 -0.09963966 1.6070600 -0.5198466
KORKOLA_CHORIOCARCINOMA_UP -0.3744594 1.47839993 -0.77812840 -0.2217174 0.83857394 -3.22690712 -1.70821076 -1.8247392 -1.096790972 0.7766130 0.106430602 1.53596539 1.48267931 0.3337191 -0.10364576 0.33957176 0.78113867 0.08030119 -1.7081769 -0.9363552 2.19093776 2.26944769 0.71838354 -0.24247756 -1.29633819 0.701466602 0.09347977 1.4125416 -1.8054660 -0.61006004 1.4158132 0.45544767 0.58758936 -3.0940532 1.23411751 0.5310415 -0.3361331
KORKOLA_SEMINOMA_UP -2.9340089 0.09586312 -0.67073745 0.4686024 0.58281055 -1.86617285 -1.39432462 -3.8666739 1.166840265 1.9282066 0.806977219 2.90705383 0.99184039 0.1234681 -0.96569590 -1.16396240 0.28761478 2.57697201 -0.8848146 0.8255735 0.58071491 -0.18386443 -0.64027729 -0.33107070 -2.65069999 -0.739030827 0.26850943 0.6218152 -1.5319993 -1.03372781 1.5970938 1.42233007 2.14424171 -2.9444395 2.36223981 2.5275209 -0.4847880
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP -0.1871021 -2.72933254 2.10389786 -1.5218035 -0.24851512 -1.94879594 -0.11225920 1.3387953 2.092476554 -0.5027557 -0.734496247 1.48332203 -2.06908392 2.1504269 1.57346111 -2.67286549 0.55601780 1.75728633 1.0591640 -3.5172751 0.41769901 -0.15799519 0.10733345 -1.26412040 0.62132681 -1.068445939 -0.81184190 1.7795510 2.8672636 0.51834308 -2.2301655 -1.72721639 1.30982203 0.7498270 -2.26434985 1.7641941 1.5182121
HOLLMAN_APOPTOSIS_VIA_CD40_UP -0.7820872 -2.13675642 3.39698951 -2.1548508 0.90823798 1.87534780 1.18216325 -0.3454263 0.519486282 0.7495966 -0.702832818 2.65768682 -1.39601416 2.9377153 0.01460505 -3.73008343 -0.30955544 2.04220857 -2.8652428 -3.1013878 0.38820637 -1.85976238 0.14583211 1.54497828 -0.51769728 0.030388041 -1.27655961 -0.1068228 0.1140717 0.19735404 -1.8393420 0.06094494 1.18064262 1.7171987 -0.09629675 2.0372182 -0.4801540
LIU_PROSTATE_CANCER_UP -2.7418994 0.36658204 -3.31691584 1.3184501 2.30781570 0.78372138 -2.49394355 -5.4987675 -0.822790802 -1.2417137 0.174898665 -0.25341599 3.10520813 -3.4272596 -2.36564481 -1.46486084 -3.27025426 1.45149707 -1.9796783 -0.2385052 -0.10360642 0.41913964 1.31326282 2.25499078 -0.48834592 1.569427440 3.08573035 0.6747347 -2.1158608 0.88924255 2.5723039 2.39831139 3.32890627 0.5872895 3.74319390 1.1868815 -1.7081250
LIU_SOX4_TARGETS_UP -0.3751389 -1.95588700 -0.83556096 2.8406515 2.03541886 1.67651015 -0.06264359 1.0278755 -0.621726452 0.1542651 2.093682904 -1.12917548 -2.22483713 -1.1771779 1.46468782 -0.49621654 -0.06320445 -1.49441905 1.4408110 1.3723181 -2.65175416 -5.32222009 -1.90422195 1.32712098 0.41560025 -0.141050306 0.65594298 -0.6743251 0.5105999 2.58778466 -1.0269048 -0.06555656 -0.16265033 2.7736846 0.23669453 -0.9452083 0.7162302
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP -1.2464061 -2.52190564 0.34481699 0.6136117 4.14525942 1.31851001 -1.50928145 -3.5261653 -0.376143666 -2.1419889 0.263685045 0.03051013 2.23927375 0.2887824 0.30432686 1.08666353 -1.81678277 2.91665062 -0.4815280 3.7840202 -1.28255238 -0.92708160 -1.47494702 0.36348866 -1.35695710 -1.365236115 -0.09332459 0.6773143 -3.3005646 1.08982967 1.3469267 -0.15650030 1.18988291 -0.1304936 -0.41848104 5.7424208 -3.6196334
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP -3.8776379 -1.06789926 -7.00642158 5.2446555 1.06812916 1.14091106 -1.23350873 -7.0151593 0.787783143 -2.2876206 4.506629996 -0.82513916 -0.50395314 -2.3986535 -1.14874866 -3.70233709 -0.71755286 -1.99280231 -1.4519194 1.8781710 -5.50515340 -3.26577909 -6.14460283 3.77798602 1.26457017 -2.522562013 2.00592405 2.4181014 -3.8502790 6.01626665 3.2565317 1.33592939 2.78983801 6.8105203 5.47203316 7.8148200 -1.0710708
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP -0.5530494 0.91449001 -5.10684798 5.8892478 0.70327111 0.68010952 -1.35401240 -4.1731715 0.829970887 2.0186035 0.734848132 -0.53350919 3.00824815 -1.7128629 -2.31656387 -1.10739140 -1.78453464 -1.33346346 -0.1610865 0.1636164 -4.61596682 -0.04388835 -2.22820486 3.50293537 1.08838500 -0.856531524 1.18347365 0.7537940 -3.2931554 -0.12534415 2.1550084 1.22544443 0.02188584 3.0547016 4.00283815 0.7785386 -1.4098262
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP -1.0842740 1.15191033 0.19359086 -0.2177736 -2.01743872 -0.35397625 -0.86551082 -0.6587418 -1.482192451 0.5834861 0.095377824 -0.80250318 -0.03850151 0.1414836 -1.48102277 0.70702073 0.54101179 -1.89001468 -0.1428820 -0.2992931 0.06876902 -1.27262670 -0.73299530 0.15317029 -0.21894175 -0.995729217 0.31049138 1.3867304 0.8623611 2.09995277 -1.6338695 0.65923937 0.40301566 2.6698444 1.87944620 0.4256969 1.8556888
FOURNIER_ACINAR_DEVELOPMENT_LATE_UP -0.6904303 1.93458550 -1.99458125 1.5799006 -0.04746809 1.35845690 1.35954571 -1.3239543 0.183594189 -0.7304046 -0.867718542 -0.16037922 1.01551852 -1.2458131 0.36381625 -0.77975659 -0.36807781 -0.37384028 0.5956824 1.1883224 -0.48945985 -0.09633758 -0.76459822 0.07532145 -0.07071889 -0.592753031 0.03215539 0.4208453 -1.3262166 0.06108885 1.8490292 -0.26820419 -0.03938847 1.1315785 2.00315374 -0.7778437 -2.1446504
FRASOR_TAMOXIFEN_RESPONSE_UP 0.5413132 1.28746036 1.36441186 3.3368271 -1.31891545 1.57406315 0.31091232 -1.8851886 -1.508855984 -0.2751830 -0.859463551 -0.54855067 3.08124648 -2.9190068 -2.21050219 -1.68670629 -1.28382294 -0.29745413 0.4018516 -0.7913413 -2.31590360 -2.18097162 -0.89954411 1.44692469 0.04672709 -0.343429133 0.79945007 0.2049267 -0.4953848 0.11145147 0.2050700 0.26420024 0.55065832 1.2372609 3.15265775 1.3700061 0.5328047
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP -2.6864978 3.43756903 -8.37492717 3.4513206 0.39310486 2.00425397 -0.88377471 -6.5962386 -1.122346365 -3.3992922 1.699856481 -1.83778409 1.82943931 -1.0046215 -2.58511818 0.68047190 -2.39298391 -4.23623360 -0.4038435 3.2643617 -5.42149983 -0.47681907 -2.08912701 3.41957446 0.43726984 -2.000731185 4.26612070 1.7425539 -3.2522439 1.90242944 7.7104250 1.33084413 0.94700410 2.9575476 6.54983238 1.8646617 -1.1245584
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP 0.7708646 1.64610911 2.90389826 -1.5098526 0.68514559 -0.62856125 1.44344048 -3.6093879 3.733916242 5.8656510 1.554307033 3.80813115 -4.74817478 0.9967577 4.21335589 -3.79160251 -0.27816578 2.15737725 -2.0032367 -3.5666508 -0.60209057 -1.95764050 -4.09387535 -4.91121565 -1.31860793 0.004839387 -0.71339502 -0.6991190 -3.9212620 0.20648249 4.1143265 4.94718475 2.97327802 4.4147432 -1.74889853 -0.4990265 -5.8390450
WATANABE_COLON_CANCER_MSI_VS_MSS_UP -1.7007583 0.25210547 -2.98028816 4.3616661 0.78884983 0.07233832 -1.40118606 -2.8961949 0.004100867 -1.1888170 -1.104752765 -1.38781767 3.19210792 -1.1626383 -2.68443406 -0.86437807 -0.25770287 -1.21047088 -1.4287985 -0.5138995 0.58785731 1.62059758 0.58826582 2.11523939 0.95256194 3.100843936 2.98714276 -0.5977086 -1.5766500 -1.05054331 1.8346936 -0.50176549 0.33463179 0.9073378 3.12400300 -0.2618967 -2.0536422
>
GSVA.Rcheck/GSVA-Ex.timings
| name | user | system | elapsed | |
| computeGeneSetsOverlap | 0.05 | 0.02 | 0.05 | |
| filterGeneSets | 0 | 0 | 0 | |
| gsva | 1.11 | 0.09 | 1.12 | |
| gsvaParam-class | 1.14 | 0.20 | 1.36 | |
| igsva | 0 | 0 | 0 | |
| plageParam-class | 0.78 | 0.24 | 1.02 | |
| ssgseaParam-class | 0.83 | 0.18 | 1.01 | |
| zscoreParam-class | 0.80 | 0.18 | 0.97 | |