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This page was generated on 2024-11-28 09:59 -0500 (Thu, 28 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences" | 861 |
| 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 109/216 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| GSVA 2.1.2 (landing page) Robert Castelo
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
|
To the developers/maintainers of the GSVA package: - 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: 2.1.2 |
| Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:GSVA.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings GSVA_2.1.2.tar.gz |
| StartedAt: 2024-11-28 08:53:03 -0500 (Thu, 28 Nov 2024) |
| EndedAt: 2024-11-28 09:00:14 -0500 (Thu, 28 Nov 2024) |
| EllapsedTime: 431.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GSVA.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:GSVA.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings GSVA_2.1.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/GSVA.Rcheck’
* using R Under development (unstable) (2024-11-14 r87333)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GSVA/DESCRIPTION’ ... OK
* this is package ‘GSVA’ version ‘2.1.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘GSVA’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 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 loading without being on the library search path ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
GsvaExprData-class.Rd: dgCMatrix-class, ExpressionSet-class,
SummarizedExperiment-class, SingleCellExperiment-class,
SpatialExperiment-class
GsvaGeneSets-class.Rd: GeneSetCollection
GsvaMethodParam-class.Rd: GeneIdentifierType-class,
GeneIdentifierType
geneIdsToGeneSetCollection.Rd: GeneIdentifierType, CollectionType,
GeneSetCollection, GeneSet, geneIds
gsva.Rd: BiocParallelParam, dgCMatrix-class, ExpressionSet,
SingleCellExperiment
gsvaAnnotation.Rd: ExpressionSet-class, SummarizedExperiment-class,
GeneIdentifierType
gsvaParam-class.Rd: GeneIdentifierType-class, GeneIdentifierType,
ExpressionSet, SummarizedExperiment, SingleCellExperiment
gsvaRanks.Rd: BiocParallelParam, dgCMatrix-class, ExpressionSet,
SingleCellExperiment
guessGeneIdType.Rd: GeneIdentifierType
plageParam-class.Rd: GeneIdentifierType-class, GeneIdentifierType
readGMT.Rd: GeneIdentifierType, getGmt, GeneSetCollection, GSEABase
ssgseaParam-class.Rd: GeneIdentifierType-class, GeneIdentifierType,
ExpressionSet, SummarizedExperiment, SingleCellExperiment
zscoreParam-class.Rd: GeneIdentifierType-class, GeneIdentifierType
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
readGMT 10.424 0.363 10.791
* 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’ ... OK
Running ‘test_plage_newapi.R’
Comparing ‘test_plage_newapi.Rout’ to ‘test_plage_newapi.Rout.save’ ... OK
Running ‘test_ssgsea_newapi.R’
Comparing ‘test_ssgsea_newapi.Rout’ to ‘test_ssgsea_newapi.Rout.save’ ... OK
Running ‘test_zscore_newapi.R’
Comparing ‘test_zscore_newapi.Rout’ to ‘test_zscore_newapi.Rout.save’ ... OK
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/GSVA.Rcheck/00check.log’
for details.
GSVA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL GSVA ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’ * installing *source* package ‘GSVA’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’ gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cli/include' -I/usr/local/include -fpic -g -O2 -Wall -c ecdfvals.c -o ecdfvals.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cli/include' -I/usr/local/include -fpic -g -O2 -Wall -c kcdfvals.c -o kcdfvals.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cli/include' -I/usr/local/include -fpic -g -O2 -Wall -c kernel_estimation.c -o kernel_estimation.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cli/include' -I/usr/local/include -fpic -g -O2 -Wall -c ks_test.c -o ks_test.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cli/include' -I/usr/local/include -fpic -g -O2 -Wall -c register_cmethods.c -o register_cmethods.o gcc -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/cli/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -shared -L/usr/local/lib -o GSVA.so ecdfvals.o kcdfvals.o kernel_estimation.o ks_test.o register_cmethods.o utils.o installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-GSVA/00new/GSVA/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** 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 Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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")
Running unit tests for GSVA C code without missing data.
Running unit tests for GSVA C code with missing data.
! Input expression data has NA values, which will be discarded from calculations.
Running unit tests for GSVA ranks.
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.
Running unit tests for ssGSEA.
RUNIT TEST PROTOCOL -- Thu Nov 28 08:56:33 2024
***********************************************
Number of test functions: 10
Number of errors: 0
Number of failures: 0
1 Test Suite :
GSVA RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10
Number of errors: 0
Number of failures: 0
> options(warn=oldWarnOptionValue[["warn"]])
>
> proc.time()
user system elapsed
10.203 0.719 10.933
GSVA.Rcheck/tests/test_gsva_newapi.Rout
R Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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.
>
> ## 2024-10-25 regression test script for method GSVA
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2024-10-25)
> 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 1.1025783 -0.9348073 1.2604604 -0.5213579 -0.1449497
g2 1.1178965 -1.1697762 -0.6188039 -1.5167080 -1.1104456
g3 -1.8181019 -1.1516529 0.9891236 -1.0173901 0.7009874
g4 -0.1944140 -0.3479166 -0.7471371 -0.6796938 1.5027270
g5 -0.6131956 1.0524922 -0.5313147 0.6119898 0.3619898
> 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 -0.28892445 -0.1890779024 -0.09887798 0.042749672 0.214636278 0.26842738 0.03925805 0.08159576 0.23619630 0.203682088 -0.028073607 -0.05134135 0.22331459 -0.2899147161 0.18007510 0.304830139 0.040125792 -0.217503733 -0.085258184 -0.0373244594 -0.544385539 -0.294674615 0.284386670 0.002037441 0.308324229 -0.179003143 0.033650341 0.191906543 -0.485544449 -0.01161912
gs2 0.07000319 -0.1736216641 -0.11233070 0.025865528 0.273808390 0.03989980 0.06091625 0.16612188 0.01797190 0.211363139 0.055277708 0.01761223 -0.12671209 -0.1719220703 0.14427310 -0.088173914 -0.045867729 -0.118569930 0.217358814 -0.0004010719 -0.001509425 -0.112020654 -0.210654480 -0.082729810 -0.031553083 -0.098474828 0.085783477 -0.067759057 -0.063875902 -0.10891681
gs3 0.08040565 -0.0932371828 0.15483344 -0.026442421 -0.081003307 0.26108419 0.19398867 0.05791899 -0.06035944 -0.085586510 0.053011873 -0.08677199 -0.17711279 -0.0457347807 0.08370679 0.061415686 -0.074178938 0.209650582 -0.065069873 -0.1897389936 -0.068618569 -0.051118415 -0.015287269 -0.080698598 -0.183500788 -0.063471749 0.063480251 -0.048050407 -0.114820815 0.03099348
gs4 -0.13413460 -0.0559817644 -0.14472382 -0.377098802 -0.077017967 0.52116800 0.24794376 -0.24065536 0.27568534 0.246390290 -0.296442690 -0.24308360 0.21995140 -0.0669631203 -0.28857658 0.288487554 0.175453532 -0.195028506 0.301734268 -0.2416538448 0.135438221 -0.149948696 0.123067153 -0.084983282 -0.503916929 0.244077635 0.223898938 -0.188320825 0.131094312 0.06702424
gs5 0.13632021 0.0257758504 0.26682546 0.215481209 -0.002094607 0.15685928 -0.20872662 0.14580686 -0.06234764 0.007704154 -0.054015919 0.10500247 -0.06789612 0.0351551598 -0.04447113 -0.130507563 -0.103724575 -0.249634876 -0.018642403 0.0675954154 0.188442269 -0.023973766 0.108192788 0.001482382 -0.124673087 -0.009086476 -0.007046928 -0.065901772 -0.313572835 -0.02129310
gs6 0.21689200 0.0769878021 -0.10900864 0.110587382 0.204888981 0.04231330 -0.34513436 0.18381969 0.05771530 -0.108784105 0.171370027 0.14286252 -0.04428696 -0.0872480777 -0.02277969 0.002250481 -0.202400347 -0.124971776 0.072824118 0.0389304790 0.097092795 -0.113128156 -0.144725793 0.141928327 0.023770092 -0.127980675 -0.096243234 -0.020188673 0.159557521 -0.10619539
gs7 0.17405701 -0.1525994651 0.06995248 -0.092261411 0.066031012 0.24120042 0.18989651 -0.14380972 0.17291747 -0.143054962 0.070204226 -0.20835320 -0.06477498 -0.2209882823 0.05262749 -0.074970924 -0.195686001 -0.166348145 0.100903990 -0.0572688553 -0.064381905 0.273394871 -0.106475192 0.017468942 0.085978013 0.215409273 -0.034489749 -0.044142411 -0.147167518 0.23852968
gs8 -0.10079372 0.1220890090 -0.06811945 -0.111623557 -0.144603524 0.04043338 -0.08254887 0.18884415 0.18017415 0.029591448 0.131986702 -0.12366040 -0.01883954 0.1384504109 -0.15871280 -0.097547001 0.197046350 -0.033602268 0.078100461 -0.0477953650 0.098798046 0.105115635 0.002369819 -0.260890342 -0.208130553 0.017531704 -0.040289940 -0.016668570 0.082968449 -0.07992436
gs9 -0.13264777 -0.3744908529 -0.08615094 -0.068909535 -0.068646790 -0.20907316 0.17959333 -0.25346378 0.02929577 -0.189680669 0.243866659 -0.22264017 0.06475953 -0.1668412394 0.14646665 -0.092098098 -0.034705321 -0.156479915 0.089437675 0.2132133691 0.080997881 -0.095437266 0.218371413 0.018017604 -0.088261720 0.091752299 0.206283048 0.046959718 0.248945767 0.46642590
gs10 -0.47243863 -0.0045356879 0.25962307 -0.283918717 0.056678179 -0.29020680 0.36651978 0.06734423 -0.31323742 0.353523199 -0.307858498 -0.11747326 -0.47983238 -0.3076697122 0.02766813 0.154646172 -0.315315173 0.399982094 -0.181549836 0.1784340072 -0.088722146 0.239041716 -0.432871403 0.207728207 0.066908632 0.454730484 0.091100210 0.418978213 0.201346364 0.13368456
gs11 0.06407443 0.1759376975 -0.03026018 -0.005850331 0.003110900 0.07343726 -0.11806219 -0.09595226 0.05250048 0.078552373 -0.059796962 -0.03583485 -0.07513965 -0.1487787966 0.26125177 -0.037796724 0.055648273 0.001067367 0.002232222 -0.0845019794 -0.045410252 -0.059549935 -0.038116513 0.024585213 0.147927155 -0.222990011 -0.096888942 -0.016722736 0.121265723 0.22093396
gs12 -0.15057967 0.0362617787 -0.13860082 -0.207938667 0.012422903 0.13177093 0.02818016 -0.08876212 0.05556861 -0.029566325 -0.136908193 0.12172244 -0.11072029 0.0056538361 -0.06158885 0.014015386 0.149784088 -0.051807574 -0.063918807 0.0906718715 -0.010440868 -0.060922773 0.060590322 -0.022315497 0.101551299 -0.047391834 0.106514246 0.071847110 0.172425914 0.09675428
gs13 0.13768941 -0.2385615869 -0.02095821 -0.077066659 -0.307300569 -0.14928671 0.36188461 0.22710925 0.17404138 -0.100841125 -0.045283907 -0.07183513 0.16144312 0.1175100304 -0.04056954 -0.151777874 0.265120188 0.012020987 0.096591668 0.1769105374 -0.152174383 0.128306317 0.030065030 -0.337358680 -0.374442914 -0.126794367 0.188302567 0.207466307 0.184335500 -0.06583723
gs14 -0.26793396 -0.1808606235 0.30535530 0.127883390 -0.060310438 0.08679883 0.15612104 0.16247758 -0.04735649 -0.081250466 0.013484139 -0.16001040 -0.36121461 0.0385335033 -0.10672540 0.127141284 0.042076755 -0.144275644 -0.050560530 0.1127201809 0.168021942 -0.100337753 0.064553084 0.060035488 -0.008801486 0.057615493 0.094644217 -0.058523336 0.035435747 0.21884723
gs15 -0.09162597 -0.1070568919 -0.05295087 0.089942030 -0.056413165 0.14504317 0.08833557 -0.03301452 0.02069414 -0.070668805 0.065358020 0.12307465 -0.05058192 -0.0731732193 0.14981230 0.076220972 -0.113817013 0.025077571 0.119076944 -0.1615862673 -0.018329544 -0.018149690 0.078108795 0.178261116 -0.082148835 -0.044405514 -0.075636382 -0.038350721 0.001808009 0.03572120
gs16 -0.06199765 0.0860599259 -0.05988112 -0.004230160 -0.084906369 -0.03777934 -0.03013568 0.12097604 -0.05597871 0.102860165 0.037568933 -0.04704989 0.19719096 -0.0521889743 -0.06610393 -0.042159104 -0.087505628 -0.258259876 -0.014858945 -0.2244530588 -0.036504666 -0.206091802 0.164321798 -0.114270100 -0.045369737 0.049074322 0.132046354 0.205780512 0.196464509 0.13608847
gs17 0.07051478 -0.1423797312 0.05147006 0.182507528 -0.018787746 -0.01812354 0.14696370 -0.13230587 -0.10515411 -0.085280731 0.043388567 -0.03525359 0.05948041 0.1097771685 -0.01507890 -0.091767764 -0.111896678 -0.329642211 -0.098553881 0.1784278634 0.257678218 -0.005347973 0.040719534 0.158395842 0.163277534 -0.120256456 0.028307723 -0.007758153 -0.047991555 -0.03796556
gs18 -0.05334806 -0.0007993417 -0.18827339 0.080971282 0.063842755 0.01831550 0.05746682 0.15493632 -0.23563627 -0.017731165 0.095381811 -0.06850576 -0.15586877 0.0633721664 0.01688851 -0.129491375 -0.093117516 0.092133659 0.146443431 0.1054195746 0.113146312 -0.010988097 0.091008011 -0.057970590 -0.017058943 -0.076718649 0.031311489 0.092440935 -0.016085124 -0.12969861
gs19 0.27057177 -0.1231162862 0.07377792 -0.194579656 -0.283561074 0.15314864 -0.06126820 0.05615526 0.36038065 -0.240198203 -0.539793304 0.17933897 0.21741131 -0.2484026076 -0.06353310 -0.189726109 0.086438327 0.255422197 -0.119312911 -0.5064675321 -0.170768101 0.330049590 0.366130269 0.297175433 0.229118367 0.073994753 0.349287253 -0.193711003 -0.267552951 -0.25009763
gs20 -0.08069187 -0.0276514971 -0.03527900 -0.075486283 0.019717102 -0.13863922 -0.17041259 0.27460661 0.24764635 0.037698325 0.025175175 -0.17862450 0.24499456 0.0308634645 -0.09379617 0.023460903 0.299683439 -0.199661176 -0.210705564 -0.0790214211 0.272321135 0.154786179 0.040506345 0.238208204 -0.206824492 -0.315480029 0.173605178 0.114592978 -0.430723605 0.10737704
gs21 0.04974287 0.1045169885 -0.04078471 0.049373719 -0.111609141 -0.04828582 0.02706050 0.13471147 0.02504339 -0.083242878 -0.206648332 0.04629951 0.21474310 0.0646595518 0.09562085 -0.105027731 0.107266343 -0.039035392 0.031661480 -0.1487894488 0.064414778 -0.108333251 -0.069906781 0.034911978 0.113824847 -0.017578112 -0.078587174 -0.073725850 0.046604635 -0.14549191
gs22 0.31405931 -0.0596481727 0.11705950 0.034359676 -0.031277438 -0.06222767 -0.23045084 -0.01859711 0.01239405 0.044499555 0.351706085 0.22312094 0.07793459 -0.0005072652 -0.09422643 -0.029527693 -0.198726571 -0.304512827 0.211732943 -0.0140233097 -0.397785136 -0.368238520 -0.495057853 -0.256806789 0.154054078 0.169349888 0.202245418 -0.041164290 0.186956214 0.12347857
gs23 0.08946965 0.1235351969 -0.17948785 -0.210338121 -0.220166089 0.19138005 0.06238147 -0.13583311 0.12533268 0.120820212 -0.061268518 -0.13587701 -0.02819000 -0.0599284817 0.00461690 0.046570594 -0.092506892 -0.025193488 0.051911802 0.0964816725 0.077018815 -0.140898972 0.081642209 0.170304546 0.077900905 0.054145662 -0.097085512 0.223174180 -0.011135158 0.04921891
gs24 -0.06417467 -0.0149414733 -0.08825404 0.086663457 0.185635477 0.24803952 0.16026007 0.10322638 0.02203439 -0.086011354 -0.129393085 -0.07842642 0.05780942 -0.1641645916 -0.10844166 0.083523235 -0.005798852 0.049678102 0.157266164 -0.0530892790 -0.050186444 -0.029898637 -0.170267017 -0.203907801 0.055094962 0.151741113 -0.032774659 0.036993512 0.209782482 -0.25139183
gs25 0.04504363 -0.1477678435 0.06123978 0.030875101 0.006332271 -0.05142798 0.06244151 0.05938117 -0.05051385 0.102790865 0.009997114 -0.16018833 -0.16674864 0.0557757709 -0.02957331 0.007140476 -0.052433844 -0.019786407 -0.092644442 -0.0348063949 0.052160702 0.237650728 0.121105480 0.007749387 0.005139870 -0.067654482 -0.001748424 -0.080777781 0.146366359 -0.07803001
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> ## until the updated GSVAdata goes through the build system
> ## remove duplicated rows
> fnames <- featureNames(huangArrayRMAnoBatchCommon_eset)
> mask <- duplicated(fnames)
> huangArrayRMAnoBatchCommon_eset <- huangArrayRMAnoBatchCommon_eset[!mask, ]
> pickrellCountsArgonneCQNcommon_eset <- pickrellCountsArgonneCQNcommon_eset[!mask, ]
>
> 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)
> 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 -0.14230367 -0.315422586 -0.391252778 0.21314789 0.398273101 -0.02979645 0.17463104 0.267085366 0.197413154 0.07317030 0.0151842356 0.27511240 0.0810594643 -0.10663006 -0.191364179 -0.30618220 -0.25336772 -0.371841240 0.131350533 0.121203177 0.19187367 -0.453188679 -0.23038804 0.10202697 0.13430550 -0.007922221 0.16012876 -0.1026394845 -0.19874779 0.201905986 0.379079882 0.288111160 0.003129612 -0.36268779 0.109323303 0.25876115
KEGG_CITRATE_CYCLE_TCA_CYCLE -0.20050240 0.251659171 0.012907911 -0.23516857 0.167389776 -0.18868132 -0.09560810 0.023323070 0.253204612 -0.29805871 0.3431470095 0.11991763 0.1565766061 0.43928238 -0.115310950 -0.41021070 -0.51450945 0.101191356 0.022557303 0.212326603 -0.29059095 -0.366166646 0.19519820 0.34074454 -0.29218845 -0.137564423 -0.03874015 -0.0460878609 -0.15938696 -0.197978984 0.005781405 0.139048823 0.376558877 -0.11695718 0.398691360 0.08538487
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.13532736 -0.345433492 0.011710140 0.10461510 0.533833683 0.08497909 -0.07344553 0.339736015 0.185290991 -0.01914787 0.3436538099 0.15113342 0.0435975273 0.34068607 -0.320374734 -0.12343554 -0.52009025 -0.079637040 0.245999513 0.006539003 0.29725419 -0.494264566 -0.37543565 0.04379510 -0.10577650 -0.067638603 0.07219409 -0.1346995651 -0.28420602 -0.008962224 -0.009796505 0.408486750 -0.058106310 -0.20736744 0.134989826 0.33162025
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS -0.04674354 0.263195829 -0.247770620 -0.57095581 -0.151561771 -0.12045011 -0.22560104 0.154107744 0.171422759 -0.41538904 0.4061269795 0.32836635 -0.3398766485 0.45244001 0.238518510 -0.52846452 0.06897794 0.239050610 0.197501686 0.196563817 0.19246698 -0.281678574 -0.14631769 -0.07506140 -0.17403834 -0.357561908 0.19240461 0.4639167217 -0.30857693 0.066925762 0.107648843 -0.244720710 -0.001734512 -0.15569292 0.158727246 0.17601071
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM -0.05032619 -0.258191115 -0.272637165 0.02525198 0.465148979 -0.07264436 -0.08922090 0.179778439 0.176454883 0.08577523 0.1956641902 0.03330815 -0.0389123845 0.21832430 -0.058259416 -0.21799128 -0.41770899 -0.167326797 -0.116287665 0.028178393 0.18546795 -0.006915134 -0.35946143 0.04791420 0.12817416 0.320065055 0.14820768 -0.3569579979 -0.32557325 -0.201263232 0.257115785 0.243139572 0.180855314 0.04036292 0.077337949 0.11527875
KEGG_GALACTOSE_METABOLISM -0.50995845 -0.329079468 -0.339175575 0.17973234 0.589347614 -0.05162470 -0.02715106 0.011294677 0.114013797 0.20364017 0.0764356949 0.18293872 0.1712761979 0.09906587 -0.421107554 -0.30991624 -0.40972409 -0.552561906 0.134900019 0.312563354 0.40474331 -0.315001807 -0.45834570 0.24600213 0.36614165 -0.301648195 0.46863888 -0.1203792148 -0.47812544 -0.138757200 0.179735274 0.362123024 -0.116536784 -0.27757268 0.332831363 0.57291951
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.39703075 0.102716763 -0.055758439 0.31975221 0.117864410 -0.47757507 -0.27421719 0.489639438 -0.092044451 -0.05615840 -0.0733668926 -0.21507390 0.1917605063 0.31436950 0.036531537 0.05068651 0.06931287 -0.242851457 -0.076828096 -0.137640062 -0.70426332 -0.249548739 0.04489322 0.16341080 0.10221980 0.200025490 -0.62964039 -0.0648658968 -0.42547266 0.070369223 0.327559970 -0.007865333 0.202249029 0.02620757 -0.341097439 0.31102195
KEGG_FATTY_ACID_METABOLISM 0.03499557 0.183481630 0.209868940 -0.24526403 0.208740708 -0.11867729 -0.23905993 0.499149905 0.389621617 -0.20723774 0.1003775624 0.28752464 0.0264952630 0.13270380 -0.078963095 -0.35370866 -0.26220000 0.023136891 0.091846094 0.130728497 -0.32229224 -0.044506799 -0.17713704 0.13893632 -0.29212370 -0.120188772 -0.42197883 -0.1038247609 -0.09705027 -0.116454060 0.246489111 0.136899664 0.489237584 -0.07581183 0.016507828 0.03745853
KEGG_STEROID_BIOSYNTHESIS 0.20009807 -0.181590600 -0.495057872 -0.25999420 0.190318716 -0.32380418 0.40236927 0.555545362 0.335883859 -0.30628334 0.0994301550 0.02953368 -0.3429990844 0.33510274 0.482927930 -0.46774054 -0.41087983 0.363293352 -0.317192255 0.185389439 0.06846786 -0.460804383 -0.03811268 0.10386440 0.18840391 -0.277020767 -0.31775356 -0.3350533324 0.04572225 0.498123402 0.204400076 0.258186496 0.104633531 0.32977002 0.105979796 0.04778385
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS -0.22614949 0.327895536 -0.044963402 0.34520160 -0.324080107 -0.37005067 0.38061477 0.506003656 -0.277633599 -0.46620361 -0.3553865693 0.38408513 -0.1610969650 0.32344843 -0.391809219 -0.04010219 -0.34840499 0.440076802 -0.553451905 0.333395458 -0.41467805 0.088706867 0.11559089 0.49584759 -0.18691696 -0.289465112 -0.25327459 0.4882409667 0.48875862 0.684163843 0.405809338 -0.411231653 0.071450744 0.46791088 -0.051584981 -0.05530372
KEGG_STEROID_HORMONE_BIOSYNTHESIS 0.36671210 -0.044753334 -0.314703043 0.36116780 -0.116640526 -0.57441058 0.06518260 0.124107112 -0.153795570 -0.03460938 0.2548813094 -0.25833519 -0.1929012102 -0.01705796 0.005540414 0.20204739 0.07500285 -0.152295626 -0.175847740 0.169535820 -0.31054108 -0.288247072 -0.32233172 0.25541302 0.10269411 -0.242164220 -0.02773543 0.1147712590 0.20472937 0.091114751 0.444999725 0.138202887 -0.099910183 0.19770815 -0.322877108 0.38977634
KEGG_OXIDATIVE_PHOSPHORYLATION -0.44463189 0.405657198 0.315892634 -0.38462194 -0.063028804 0.20080896 -0.22585921 0.041829730 -0.078383761 -0.04923779 0.3668914393 -0.09328146 0.1964486364 0.31315273 -0.186534968 -0.36302054 -0.30193772 0.313561618 0.235744939 -0.322548387 -0.29735863 -0.198843886 -0.08765849 0.26407152 -0.24776804 0.241277903 0.12809953 -0.2093056215 -0.13991504 -0.165510760 0.004363026 0.173885611 0.285551064 -0.03747100 0.350960284 -0.14799876
KEGG_PURINE_METABOLISM -0.12429947 -0.003146735 0.109750349 0.02407314 0.152251724 0.20601792 0.04975895 0.087671238 -0.162044311 -0.08810469 0.2675309252 0.13421712 0.0005983356 0.19999998 -0.016663670 -0.19442126 -0.19597096 0.160113602 -0.004919668 -0.160288451 0.05043435 -0.238070609 -0.19697287 0.06490013 -0.20201793 0.064661415 -0.02823185 0.0008141729 -0.03520901 -0.008240455 0.054601543 -0.011461863 0.123583714 -0.14260536 0.001604703 -0.07538664
KEGG_PYRIMIDINE_METABOLISM -0.07969123 0.018479830 0.237335120 0.02680913 -0.007995819 0.25078444 -0.04171819 0.232922315 -0.155937293 -0.15883818 0.2909598842 0.19325236 -0.0970061662 0.19946686 0.037485420 -0.17798970 -0.14719367 0.256222265 0.019930009 -0.089948280 0.16264470 -0.308533382 -0.08200015 0.02988157 -0.30636924 0.090131040 -0.09054591 -0.1749494745 -0.09480720 -0.130857031 -0.040135166 -0.067286057 0.334271675 -0.05879758 -0.032964519 -0.17672172
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM -0.13064364 -0.065911721 -0.134222400 -0.15808267 0.026407189 -0.22107254 0.14077844 0.306640325 -0.123790795 -0.17620057 -0.1726825520 0.30252067 -0.0864643151 0.09958601 0.192126250 0.31442915 -0.31609967 -0.125684993 0.295597931 0.179207683 -0.20454937 0.057361897 -0.14883905 0.04965298 0.12243300 -0.041113555 -0.07917053 0.1816381096 -0.10277463 0.195475554 0.285753383 0.082372899 -0.370044975 -0.06073283 -0.243940084 0.22641916
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.10846488 -0.463507010 -0.180872151 0.09430933 0.244190256 -0.15405349 0.22393116 0.054212250 0.280540684 0.13649494 0.0599544061 -0.28868115 -0.0460531567 0.01265874 0.151929342 0.41789314 -0.13735320 -0.372284254 -0.406066496 0.282293938 0.19600499 -0.021052194 -0.26533358 0.12269137 0.26620757 0.058984278 0.05044338 -0.2505298486 -0.05301505 0.085669602 0.197644910 0.201488640 -0.407099059 -0.14256992 0.201256510 0.15101871
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.31330678 -0.149492749 0.003483417 0.19263550 -0.070024135 0.04076325 0.14227568 0.297635845 0.200688737 -0.18331111 0.2418556355 0.26735951 -0.2921105065 0.16958516 0.349104212 0.15204901 -0.22730835 -0.020102228 0.165816873 -0.283890575 0.23251096 -0.391190301 0.09379114 -0.22493866 -0.11044920 -0.372845225 -0.43902463 0.1716953214 0.03214754 0.168923799 -0.116190352 -0.006898610 -0.225469408 -0.18264898 0.214327770 -0.12475506
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.13821704 0.310127784 0.066445588 -0.42511864 -0.090306905 0.17837211 -0.19796655 0.347010789 0.408154036 -0.49673276 0.4127975060 0.22029835 0.2082638952 0.22095995 0.097006653 -0.28459992 -0.23839562 -0.180980405 0.227099410 0.266237949 -0.26309956 -0.366347365 -0.24746034 0.08971504 -0.26988765 -0.356087684 -0.48033192 0.2879096649 0.04729230 0.216578558 0.054749956 -0.098705529 0.327656315 -0.45815823 0.271899213 0.29958118
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.21234031 0.328164338 -0.305429769 -0.40920870 0.154270745 0.29337437 -0.24124926 -0.242270521 0.183690508 -0.57969585 0.4054083846 0.24857693 0.1309828553 0.50247869 0.270577765 0.03840523 -0.02241916 -0.145601032 0.137344238 0.442709981 0.39693964 -0.292615556 -0.12543161 -0.19155625 -0.07526516 -0.258038832 0.05263564 -0.2392736110 -0.27129310 -0.410804271 0.113044178 -0.264001250 -0.443467665 0.26368623 0.710107163 -0.01510618
KEGG_LYSINE_DEGRADATION -0.04858688 0.007615060 0.229421096 0.08925233 0.038306122 0.28980546 -0.18136349 0.186751148 0.202034280 -0.15545560 0.2126122092 0.16006097 0.2902420241 -0.09167494 0.074552004 -0.20477042 -0.11043819 -0.118851885 -0.043566480 0.235327437 0.07804014 -0.291097266 -0.01691432 -0.21943620 -0.20989917 0.076703134 -0.27596968 0.0388993077 -0.12327597 -0.055137936 -0.080184092 -0.017057734 0.003258048 -0.40132421 0.136618821 0.01103533
KEGG_ARGININE_AND_PROLINE_METABOLISM -0.22599881 0.046481159 -0.042679823 0.01685008 0.185540061 -0.31435358 0.33873171 0.146647899 -0.125142798 -0.04144693 -0.1308233076 -0.23631365 -0.0862667676 0.12265902 0.040207439 0.01955411 -0.23852570 -0.417826188 0.099780708 -0.025387365 0.06735798 0.061697207 -0.17988293 0.28098355 0.26353347 0.116707414 0.03351622 -0.2677372049 -0.11117794 0.309730283 0.208703010 0.293429518 -0.140256326 0.08662591 0.021626117 0.09297224
KEGG_HISTIDINE_METABOLISM 0.36509136 0.232658699 -0.116502900 -0.05141446 0.328105573 -0.20719131 -0.09511699 0.073873353 0.004448375 -0.21104151 -0.2754103889 -0.08738851 -0.2219436943 -0.04830135 0.222754115 0.07953853 0.10675039 0.008570392 -0.158305200 -0.207207830 -0.07062902 0.328890134 -0.03290924 -0.12579803 0.14889977 -0.369990857 -0.44130723 0.3027378486 -0.35216472 0.318584212 0.085706968 -0.328382753 0.058090870 -0.01746631 -0.141792587 -0.22080931
KEGG_TYROSINE_METABOLISM 0.20146600 0.168748206 -0.038021560 -0.19672569 -0.075048632 -0.12221566 0.33223135 -0.077860830 -0.191343952 -0.18419100 0.0009062282 -0.41370558 -0.1984151146 0.44633162 0.460112746 -0.23661823 0.06304089 0.446618130 -0.340634185 -0.263493921 0.32434436 0.147263398 -0.02495879 -0.16870285 -0.06053492 -0.228179608 -0.09131817 0.2054001200 -0.14089275 -0.124542842 0.280838580 -0.404680384 -0.005635066 0.41960567 0.045597099 -0.10641710
KEGG_PHENYLALANINE_METABOLISM 0.14987883 0.306094920 -0.425609638 0.03175427 0.007934090 -0.43992623 0.41671291 0.002250151 -0.664926010 0.33908117 -0.1346745613 -0.56306513 -0.3409626816 0.23351887 0.387413366 -0.14053193 -0.13915959 0.402187388 -0.060910823 0.196879226 0.30686970 -0.367733224 0.39944412 0.09814593 0.19222915 -0.451592015 0.02516237 0.4205597858 0.13969499 -0.168737298 0.038140347 -0.119329329 -0.453376906 0.58562092 0.154957006 -0.40567626
KEGG_TRYPTOPHAN_METABOLISM 0.02974690 0.069678200 0.164973394 -0.04936804 0.276382946 -0.39624538 -0.07475994 0.254781450 0.189667871 -0.16626755 -0.0767493207 0.10596150 -0.0679683568 0.10871564 -0.205792806 -0.07443261 -0.14722023 -0.200909073 0.338823015 0.029115397 -0.38027834 -0.188845048 0.04982826 -0.07708070 0.08733682 -0.026228617 -0.28185008 0.1056077412 -0.15419588 -0.065214119 0.059542190 -0.027720896 0.418277752 0.08051465 -0.197805216 0.01754684
> pickrellPar <- gsvaParam(pickrellCountsArgonneCQNcommon_eset,
+ canonicalC2BroadSets, minSize=5, maxSize=500,
+ kcdf="Poisson")
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
> 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 0.22812891 -0.263355222 -0.37470050 0.290732334 0.17079093 -0.45765232 0.50012601 -0.09532256 -0.47875336 0.2005760985 0.092621366 0.393690568 -0.10337215 0.25814796 -0.007047109 -0.32196546 0.54100312 0.36730644 -0.229340073 -0.21569337 -0.39089158 -0.10367966 -0.0265281455 0.206218417 -0.38405692 -0.26149665 0.11109491 -0.305540564 -0.23084358 0.119516674 0.40469862 -0.359303191 -0.2285660734 0.0670553834 -0.193418010 0.406591786
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.19353985 -0.200671800 -0.31936816 0.257300219 0.09459388 -0.14437972 0.58037080 0.22069982 -0.48416294 -0.0911133032 0.142997298 -0.013405272 0.21749563 0.14846560 0.331053799 -0.62290688 0.26557435 0.10178204 -0.243753239 -0.08360178 -0.13185028 -0.18973195 0.2221045889 -0.008182147 -0.27726362 -0.32679981 0.55375324 -0.272956015 -0.41562145 -0.238571669 0.23559980 -0.333287901 -0.4136149051 0.3504867977 -0.033474324 -0.001807616
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.39550501 -0.351321414 -0.14110425 0.358243057 0.16435766 -0.26645789 0.66763824 0.18030231 -0.55044204 0.0557952309 0.021388295 0.576276913 0.11071439 0.29896526 0.104972515 -0.50323751 0.57733745 0.46874390 -0.256221334 -0.36544895 -0.33575684 -0.39328574 0.1106353940 0.023796472 -0.34202930 -0.25875177 0.28102418 -0.433601675 -0.31440655 -0.006812749 0.26563946 -0.454982215 -0.4530852168 0.2943696221 -0.265834459 0.464109149
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.30352162 -0.233816407 -0.27160065 -0.246247207 -0.06071677 0.04536230 0.38822954 -0.15951208 0.02167093 -0.0009868643 0.156336200 -0.068057068 -0.26097473 0.47006050 0.358846550 -0.51169838 0.41369471 0.25978330 0.147722431 -0.10416667 0.29383289 -0.32583477 -0.3409895574 -0.079554856 -0.25840080 -0.55447175 0.33358642 0.470985307 -0.02891824 0.104965489 0.29526021 -0.142020689 0.3092595811 -0.0459739970 -0.268403065 0.119173232
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.11033580 -0.062206809 -0.04584560 0.442596321 -0.43860752 -0.26354440 0.47352638 0.10394622 -0.35492025 0.1683707621 0.143921586 0.214073587 0.15383886 0.01670041 0.220658935 -0.31831394 0.48932471 0.46125203 -0.425536886 -0.19921231 -0.31866404 0.01331120 -0.0384217078 -0.043444513 -0.35216375 -0.12959691 0.26961102 -0.288865569 -0.32149898 -0.241547259 0.35727062 -0.185325504 -0.3766633793 0.3981693832 -0.189099092 0.344009489
KEGG_GALACTOSE_METABOLISM 0.05968213 -0.423880642 -0.04004200 0.349477244 -0.12227027 -0.46339930 0.51695869 -0.01678146 -0.35296517 0.2445369055 0.472971320 0.344522701 0.33867856 0.24989655 0.250426294 -0.45236845 0.57775802 0.21524751 -0.336019746 -0.08788026 -0.42317686 -0.04080587 -0.2214574734 0.056153250 -0.07821159 0.07863864 0.27266698 -0.411791653 -0.36014334 -0.190298991 0.39452862 -0.533045360 -0.4125257996 0.3437504852 -0.176878763 0.513759918
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.51787543 0.042034908 -0.12451085 -0.038064187 0.31987038 -0.46521958 0.39708699 0.01144431 0.37686424 0.5270750790 -0.001858769 -0.116619796 -0.05921058 0.71771018 0.241435211 -0.28758375 0.69491752 0.45982511 0.297599608 -0.50769311 -0.41537974 -0.27260468 -0.0509472657 0.414217903 -0.23402892 -0.52793899 -0.51628394 0.447889841 -0.42312055 0.175658085 -0.07464253 0.344370366 0.2088021678 -0.3224188559 -0.391531733 0.285580764
KEGG_FATTY_ACID_METABOLISM 0.20823397 -0.241921084 -0.30379479 0.187014213 0.29338100 -0.08777247 0.52267768 0.27472038 -0.34093551 0.1468463154 0.062462542 0.085884109 0.13921725 0.51255637 0.291260701 -0.50392822 0.43325585 0.28246279 -0.303333035 -0.30577707 -0.18311108 -0.13226462 0.0150380402 0.283730125 -0.48304687 -0.50004910 0.09637623 -0.008330810 -0.31248520 0.240872277 0.20586330 -0.037848767 -0.3293889268 -0.0002619859 -0.139285035 0.340043918
KEGG_STEROID_BIOSYNTHESIS 0.33555025 0.080447197 -0.52654139 -0.264233483 0.32230491 0.07428098 0.30042368 0.29034851 -0.28507907 -0.6240119550 -0.150252031 -0.315794357 0.10365448 0.12635135 0.040393332 -0.37074397 -0.17108798 -0.02795860 -0.361857163 -0.33292803 -0.30373042 -0.19679981 0.6254377288 -0.009132700 0.19306085 0.09838023 0.13679885 -0.116683420 -0.26307803 -0.013155328 0.20258065 0.113702556 0.1627510357 0.5348554773 0.511929756 -0.189486235
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 0.15631681 0.084781957 -0.52932434 0.552990565 0.26301727 -0.59722302 0.12192049 0.47568307 0.39619228 -0.4647553926 -0.432516961 0.259251836 0.48663470 -0.03608670 -0.087762940 -0.40806006 -0.38975683 0.44392363 -0.215684354 -0.06839988 -0.20773783 0.30163867 0.2339610147 0.628355197 -0.21630584 -0.24968799 -0.29361770 0.204281767 0.38017089 0.372299022 0.35485746 0.166369614 -0.1046542740 -0.3541904396 -0.185978451 0.005576856
KEGG_STEROID_HORMONE_BIOSYNTHESIS 0.38401346 0.114401373 -0.45576082 0.356676495 -0.25638830 -0.29368341 -0.15897709 0.15045590 0.39649319 -0.0469501629 -0.117706482 -0.020320540 0.05344534 0.23711538 -0.066561132 0.25946951 0.10909131 -0.13089860 -0.209798086 -0.28930757 -0.15301440 0.38772282 -0.3239550451 0.274999683 0.25274925 0.01140588 -0.01957855 0.523475320 0.25999884 -0.202333818 0.14865078 0.497052412 -0.0003392273 -0.4017935592 -0.318178751 0.216543081
KEGG_OXIDATIVE_PHOSPHORYLATION 0.03275894 -0.066687128 -0.24411448 0.178976382 -0.07739081 0.23839051 0.53479936 0.11062943 -0.58614604 -0.1231529161 0.011086897 0.254776797 0.10757155 0.23088898 0.196978485 -0.21208191 0.13210528 0.22598485 -0.166527579 -0.12403773 0.02785705 -0.11083714 0.0482978612 -0.293151501 -0.43458192 -0.36542734 0.06548564 -0.307834152 0.24198224 -0.185694934 0.25245395 -0.015265711 -0.1000535768 0.2486890645 -0.322154550 -0.196467278
KEGG_PURINE_METABOLISM 0.20023659 -0.107367072 -0.10728443 0.291663773 -0.05283553 -0.02859522 0.36157660 0.19316332 -0.19143021 -0.1572998000 0.049080483 0.109067828 -0.11833371 0.10564365 0.139338503 -0.10233547 0.24853991 0.18038953 0.046367008 -0.21468925 -0.19907099 -0.17785664 -0.1297500619 -0.149496262 -0.20375506 -0.18721379 0.14549532 -0.025164874 0.03659184 0.032750693 -0.01289068 0.002391921 -0.1715995805 0.1037162394 -0.157361053 -0.016062020
KEGG_PYRIMIDINE_METABOLISM 0.31160686 -0.314337137 0.02465540 0.453228985 -0.07810397 0.12015916 0.43909081 0.15814096 -0.34017799 -0.0081584730 0.044825193 0.110742509 -0.26372825 0.22189578 0.248993194 -0.26563543 0.21792676 0.26036321 -0.170161658 -0.24625352 -0.26111910 -0.28286211 -0.0132632619 -0.175035994 -0.39042012 -0.27213628 0.21360327 0.007963696 0.07924093 0.141929379 -0.08314588 0.091267966 -0.2759966513 0.3117578458 -0.421748951 0.011205471
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.04137278 0.243239788 -0.16090629 0.042626922 0.40716099 0.02795095 0.08519888 0.08165140 -0.05544785 -0.2042398482 -0.079047867 -0.304524860 -0.03288761 0.11420844 0.310266126 -0.16555921 0.02341918 0.02665627 0.080941061 -0.12399840 0.09060201 0.03870403 -0.2568792442 0.215932167 -0.26034017 -0.15336446 0.26947058 0.342014672 -0.28436268 0.223771668 -0.05678723 0.114388282 -0.0220268977 -0.3108220646 0.129566526 0.237023883
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.24286149 -0.281021942 -0.11196471 0.119410270 0.17458480 -0.21600024 -0.30947266 -0.11270084 0.31554246 -0.1544698212 -0.174652441 0.009889643 -0.39356493 0.15198519 0.304577250 -0.01314328 0.02626527 -0.23588917 0.195167717 -0.14020907 -0.14552128 0.28081761 -0.0969045615 0.295113478 0.20735687 -0.09096551 0.19877101 -0.140658529 -0.05967062 0.530244229 -0.29150989 -0.018469164 -0.0648473323 -0.3563706157 0.352493400 0.245123799
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.46859153 -0.379300667 -0.01868216 0.429301488 0.17347937 -0.20479501 0.30306957 0.34379252 -0.38026186 0.0857333714 -0.259806130 -0.051601632 -0.18492935 0.51260419 0.190312676 -0.43573176 0.26676090 -0.04452266 0.005188443 -0.49904874 -0.19476281 -0.04975948 -0.1802249032 -0.187156160 -0.11882846 -0.27860347 0.06497422 0.015459913 -0.26962268 0.396055231 -0.20336841 -0.056566339 -0.2623303556 0.0218337313 -0.149172969 0.296738232
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.13165312 -0.333486357 -0.25807014 0.212746862 0.16537668 -0.28578872 0.55522995 -0.12541421 -0.32444915 -0.0908361898 0.374830896 -0.059743969 0.18262115 0.52189107 0.300491230 -0.43227506 0.36348022 0.23608991 -0.251607492 -0.24494595 -0.23020864 -0.30715338 -0.1097869254 0.335750429 -0.42776978 -0.35468076 0.05586066 -0.011469915 -0.38304181 0.190347530 0.32810277 -0.106020282 -0.2278552818 -0.0010987744 -0.009598621 0.282065377
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.34866653 -0.129961799 -0.53134605 0.413981718 0.45007503 0.07242446 0.26567130 -0.21208186 -0.37406279 -0.6432922517 0.073564590 -0.169707405 -0.19330715 0.44350590 0.326741959 -0.39438102 0.20225333 -0.22872589 -0.344279983 0.21730971 -0.03203297 -0.33343673 -0.5599649471 0.105459222 -0.11361999 -0.25714223 0.53274773 -0.177539040 -0.15373291 0.311023102 0.28440312 -0.550490532 -0.2161631449 -0.1390562905 0.142388873 0.096096749
KEGG_LYSINE_DEGRADATION 0.18494876 -0.301470123 0.14132481 -0.002621688 0.05015042 0.13622957 0.33458090 0.17109948 -0.15867468 0.0003849763 0.054067800 -0.068680732 0.19042998 0.06804951 0.394760575 -0.30703160 0.06853304 -0.30397621 0.175905945 -0.20687387 -0.14129301 -0.10296603 0.1433435814 0.077433293 -0.18303745 -0.05981301 0.15445734 -0.069524038 -0.26483337 -0.115915730 0.01319768 -0.195524378 -0.3691190823 0.0982540134 0.020016829 0.173412122
KEGG_ARGININE_AND_PROLINE_METABOLISM 0.27313717 -0.006275212 -0.20431253 0.190536329 0.26357364 -0.08986962 0.33535841 0.08369295 -0.15741845 -0.0368390006 -0.011551509 -0.200019910 0.06866612 0.30451139 0.104228306 -0.29137253 0.28990804 0.07934982 0.006305633 -0.25713144 -0.29690035 0.17278938 -0.1979099576 0.243229750 -0.25100313 -0.11679394 0.11797791 0.054808974 -0.24014345 0.340464431 0.03801927 0.119241532 -0.1700499696 -0.1940067222 -0.059602030 0.053208863
KEGG_HISTIDINE_METABOLISM 0.32853038 -0.057164812 0.23315460 0.169742425 0.01570033 0.04234044 0.14603217 -0.18993749 0.10651264 0.0512641019 -0.228100268 -0.127091012 -0.23913329 0.17260826 0.063898693 -0.07849663 0.35259850 0.03083913 0.086876963 -0.09798041 -0.25217403 0.15586151 0.0460886670 0.127022739 -0.15770660 -0.39737625 -0.45113673 0.435864620 -0.03705763 0.051361970 -0.09271126 0.345100659 0.0779934347 0.1202706083 0.115079486 -0.106774127
KEGG_TYROSINE_METABOLISM -0.01145121 -0.195656442 -0.32679481 0.236210111 -0.23229989 0.20153868 0.22237215 0.26727784 -0.23845151 0.1921011166 -0.246175280 -0.118369345 -0.42849368 0.01975597 0.004091731 0.01083809 0.38756357 0.09763915 -0.181393091 0.19996544 0.41059691 0.05418104 -0.3215846275 0.182779499 -0.31116026 -0.45651782 0.33597072 0.131423856 0.29692628 -0.170172936 0.15571905 -0.081966569 0.2428263666 -0.0315041493 0.085376038 0.152931026
KEGG_PHENYLALANINE_METABOLISM 0.17876930 0.461533646 -0.62066204 -0.141533765 0.27696353 -0.20615287 -0.26584090 0.10882765 -0.12564179 -0.1941277338 -0.595634193 -0.090748269 -0.46544720 -0.44323209 -0.094230783 0.28219191 0.09985828 -0.08156841 0.487792811 -0.06706930 0.37972732 0.56110203 -0.1060520245 0.467821351 -0.17722929 -0.17697362 0.14854319 0.651027624 0.19579886 -0.289555438 -0.55517146 0.450858905 0.3373233877 0.1943208483 -0.124553187 -0.095947712
KEGG_TRYPTOPHAN_METABOLISM 0.02561159 0.043980374 -0.31897262 0.096835151 0.12979176 -0.18708412 0.21234061 0.05343963 0.09277264 -0.1502765995 0.007712090 0.065525644 0.14490981 0.31042699 0.208687246 -0.12850955 0.16001678 -0.11682337 0.159732707 -0.40441996 -0.29936947 0.20875791 -0.0002505521 0.127602204 -0.15109245 -0.26472714 -0.09219912 0.332216918 -0.29296983 0.016344873 -0.06296213 0.330906743 0.0411330692 -0.0550424496 -0.007991669 -0.070061618
>
> 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)
> 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
47.916 1.015 48.995
GSVA.Rcheck/tests/test_gsva_newapi.Rout.save
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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>
> ## 2024-10-25 regression test script for method GSVA
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2024-10-25)
> 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 1.1025783 -0.9348073 1.2604604 -0.5213579 -0.1449497
g2 1.1178965 -1.1697762 -0.6188039 -1.5167080 -1.1104456
g3 -1.8181019 -1.1516529 0.9891236 -1.0173901 0.7009874
g4 -0.1944140 -0.3479166 -0.7471371 -0.6796938 1.5027270
g5 -0.6131956 1.0524922 -0.5313147 0.6119898 0.3619898
> 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 -0.28892445 -0.1890779024 -0.09887798 0.042749672 0.214636278 0.26842738 0.03925805 0.08159576 0.23619630 0.203682088 -0.028073607 -0.05134135 0.22331459 -0.2899147161 0.18007510 0.304830139 0.040125792 -0.217503733 -0.085258184 -0.0373244594 -0.544385539 -0.294674615 0.284386670 0.002037441 0.308324229 -0.179003143 0.033650341 0.191906543 -0.485544449 -0.01161912
gs2 0.07000319 -0.1736216641 -0.11233070 0.025865528 0.273808390 0.03989980 0.06091625 0.16612188 0.01797190 0.211363139 0.055277708 0.01761223 -0.12671209 -0.1719220703 0.14427310 -0.088173914 -0.045867729 -0.118569930 0.217358814 -0.0004010719 -0.001509425 -0.112020654 -0.210654480 -0.082729810 -0.031553083 -0.098474828 0.085783477 -0.067759057 -0.063875902 -0.10891681
gs3 0.08040565 -0.0932371828 0.15483344 -0.026442421 -0.081003307 0.26108419 0.19398867 0.05791899 -0.06035944 -0.085586510 0.053011873 -0.08677199 -0.17711279 -0.0457347807 0.08370679 0.061415686 -0.074178938 0.209650582 -0.065069873 -0.1897389936 -0.068618569 -0.051118415 -0.015287269 -0.080698598 -0.183500788 -0.063471749 0.063480251 -0.048050407 -0.114820815 0.03099348
gs4 -0.13413460 -0.0559817644 -0.14472382 -0.377098802 -0.077017967 0.52116800 0.24794376 -0.24065536 0.27568534 0.246390290 -0.296442690 -0.24308360 0.21995140 -0.0669631203 -0.28857658 0.288487554 0.175453532 -0.195028506 0.301734268 -0.2416538448 0.135438221 -0.149948696 0.123067153 -0.084983282 -0.503916929 0.244077635 0.223898938 -0.188320825 0.131094312 0.06702424
gs5 0.13632021 0.0257758504 0.26682546 0.215481209 -0.002094607 0.15685928 -0.20872662 0.14580686 -0.06234764 0.007704154 -0.054015919 0.10500247 -0.06789612 0.0351551598 -0.04447113 -0.130507563 -0.103724575 -0.249634876 -0.018642403 0.0675954154 0.188442269 -0.023973766 0.108192788 0.001482382 -0.124673087 -0.009086476 -0.007046928 -0.065901772 -0.313572835 -0.02129310
gs6 0.21689200 0.0769878021 -0.10900864 0.110587382 0.204888981 0.04231330 -0.34513436 0.18381969 0.05771530 -0.108784105 0.171370027 0.14286252 -0.04428696 -0.0872480777 -0.02277969 0.002250481 -0.202400347 -0.124971776 0.072824118 0.0389304790 0.097092795 -0.113128156 -0.144725793 0.141928327 0.023770092 -0.127980675 -0.096243234 -0.020188673 0.159557521 -0.10619539
gs7 0.17405701 -0.1525994651 0.06995248 -0.092261411 0.066031012 0.24120042 0.18989651 -0.14380972 0.17291747 -0.143054962 0.070204226 -0.20835320 -0.06477498 -0.2209882823 0.05262749 -0.074970924 -0.195686001 -0.166348145 0.100903990 -0.0572688553 -0.064381905 0.273394871 -0.106475192 0.017468942 0.085978013 0.215409273 -0.034489749 -0.044142411 -0.147167518 0.23852968
gs8 -0.10079372 0.1220890090 -0.06811945 -0.111623557 -0.144603524 0.04043338 -0.08254887 0.18884415 0.18017415 0.029591448 0.131986702 -0.12366040 -0.01883954 0.1384504109 -0.15871280 -0.097547001 0.197046350 -0.033602268 0.078100461 -0.0477953650 0.098798046 0.105115635 0.002369819 -0.260890342 -0.208130553 0.017531704 -0.040289940 -0.016668570 0.082968449 -0.07992436
gs9 -0.13264777 -0.3744908529 -0.08615094 -0.068909535 -0.068646790 -0.20907316 0.17959333 -0.25346378 0.02929577 -0.189680669 0.243866659 -0.22264017 0.06475953 -0.1668412394 0.14646665 -0.092098098 -0.034705321 -0.156479915 0.089437675 0.2132133691 0.080997881 -0.095437266 0.218371413 0.018017604 -0.088261720 0.091752299 0.206283048 0.046959718 0.248945767 0.46642590
gs10 -0.47243863 -0.0045356879 0.25962307 -0.283918717 0.056678179 -0.29020680 0.36651978 0.06734423 -0.31323742 0.353523199 -0.307858498 -0.11747326 -0.47983238 -0.3076697122 0.02766813 0.154646172 -0.315315173 0.399982094 -0.181549836 0.1784340072 -0.088722146 0.239041716 -0.432871403 0.207728207 0.066908632 0.454730484 0.091100210 0.418978213 0.201346364 0.13368456
gs11 0.06407443 0.1759376975 -0.03026018 -0.005850331 0.003110900 0.07343726 -0.11806219 -0.09595226 0.05250048 0.078552373 -0.059796962 -0.03583485 -0.07513965 -0.1487787966 0.26125177 -0.037796724 0.055648273 0.001067367 0.002232222 -0.0845019794 -0.045410252 -0.059549935 -0.038116513 0.024585213 0.147927155 -0.222990011 -0.096888942 -0.016722736 0.121265723 0.22093396
gs12 -0.15057967 0.0362617787 -0.13860082 -0.207938667 0.012422903 0.13177093 0.02818016 -0.08876212 0.05556861 -0.029566325 -0.136908193 0.12172244 -0.11072029 0.0056538361 -0.06158885 0.014015386 0.149784088 -0.051807574 -0.063918807 0.0906718715 -0.010440868 -0.060922773 0.060590322 -0.022315497 0.101551299 -0.047391834 0.106514246 0.071847110 0.172425914 0.09675428
gs13 0.13768941 -0.2385615869 -0.02095821 -0.077066659 -0.307300569 -0.14928671 0.36188461 0.22710925 0.17404138 -0.100841125 -0.045283907 -0.07183513 0.16144312 0.1175100304 -0.04056954 -0.151777874 0.265120188 0.012020987 0.096591668 0.1769105374 -0.152174383 0.128306317 0.030065030 -0.337358680 -0.374442914 -0.126794367 0.188302567 0.207466307 0.184335500 -0.06583723
gs14 -0.26793396 -0.1808606235 0.30535530 0.127883390 -0.060310438 0.08679883 0.15612104 0.16247758 -0.04735649 -0.081250466 0.013484139 -0.16001040 -0.36121461 0.0385335033 -0.10672540 0.127141284 0.042076755 -0.144275644 -0.050560530 0.1127201809 0.168021942 -0.100337753 0.064553084 0.060035488 -0.008801486 0.057615493 0.094644217 -0.058523336 0.035435747 0.21884723
gs15 -0.09162597 -0.1070568919 -0.05295087 0.089942030 -0.056413165 0.14504317 0.08833557 -0.03301452 0.02069414 -0.070668805 0.065358020 0.12307465 -0.05058192 -0.0731732193 0.14981230 0.076220972 -0.113817013 0.025077571 0.119076944 -0.1615862673 -0.018329544 -0.018149690 0.078108795 0.178261116 -0.082148835 -0.044405514 -0.075636382 -0.038350721 0.001808009 0.03572120
gs16 -0.06199765 0.0860599259 -0.05988112 -0.004230160 -0.084906369 -0.03777934 -0.03013568 0.12097604 -0.05597871 0.102860165 0.037568933 -0.04704989 0.19719096 -0.0521889743 -0.06610393 -0.042159104 -0.087505628 -0.258259876 -0.014858945 -0.2244530588 -0.036504666 -0.206091802 0.164321798 -0.114270100 -0.045369737 0.049074322 0.132046354 0.205780512 0.196464509 0.13608847
gs17 0.07051478 -0.1423797312 0.05147006 0.182507528 -0.018787746 -0.01812354 0.14696370 -0.13230587 -0.10515411 -0.085280731 0.043388567 -0.03525359 0.05948041 0.1097771685 -0.01507890 -0.091767764 -0.111896678 -0.329642211 -0.098553881 0.1784278634 0.257678218 -0.005347973 0.040719534 0.158395842 0.163277534 -0.120256456 0.028307723 -0.007758153 -0.047991555 -0.03796556
gs18 -0.05334806 -0.0007993417 -0.18827339 0.080971282 0.063842755 0.01831550 0.05746682 0.15493632 -0.23563627 -0.017731165 0.095381811 -0.06850576 -0.15586877 0.0633721664 0.01688851 -0.129491375 -0.093117516 0.092133659 0.146443431 0.1054195746 0.113146312 -0.010988097 0.091008011 -0.057970590 -0.017058943 -0.076718649 0.031311489 0.092440935 -0.016085124 -0.12969861
gs19 0.27057177 -0.1231162862 0.07377792 -0.194579656 -0.283561074 0.15314864 -0.06126820 0.05615526 0.36038065 -0.240198203 -0.539793304 0.17933897 0.21741131 -0.2484026076 -0.06353310 -0.189726109 0.086438327 0.255422197 -0.119312911 -0.5064675321 -0.170768101 0.330049590 0.366130269 0.297175433 0.229118367 0.073994753 0.349287253 -0.193711003 -0.267552951 -0.25009763
gs20 -0.08069187 -0.0276514971 -0.03527900 -0.075486283 0.019717102 -0.13863922 -0.17041259 0.27460661 0.24764635 0.037698325 0.025175175 -0.17862450 0.24499456 0.0308634645 -0.09379617 0.023460903 0.299683439 -0.199661176 -0.210705564 -0.0790214211 0.272321135 0.154786179 0.040506345 0.238208204 -0.206824492 -0.315480029 0.173605178 0.114592978 -0.430723605 0.10737704
gs21 0.04974287 0.1045169885 -0.04078471 0.049373719 -0.111609141 -0.04828582 0.02706050 0.13471147 0.02504339 -0.083242878 -0.206648332 0.04629951 0.21474310 0.0646595518 0.09562085 -0.105027731 0.107266343 -0.039035392 0.031661480 -0.1487894488 0.064414778 -0.108333251 -0.069906781 0.034911978 0.113824847 -0.017578112 -0.078587174 -0.073725850 0.046604635 -0.14549191
gs22 0.31405931 -0.0596481727 0.11705950 0.034359676 -0.031277438 -0.06222767 -0.23045084 -0.01859711 0.01239405 0.044499555 0.351706085 0.22312094 0.07793459 -0.0005072652 -0.09422643 -0.029527693 -0.198726571 -0.304512827 0.211732943 -0.0140233097 -0.397785136 -0.368238520 -0.495057853 -0.256806789 0.154054078 0.169349888 0.202245418 -0.041164290 0.186956214 0.12347857
gs23 0.08946965 0.1235351969 -0.17948785 -0.210338121 -0.220166089 0.19138005 0.06238147 -0.13583311 0.12533268 0.120820212 -0.061268518 -0.13587701 -0.02819000 -0.0599284817 0.00461690 0.046570594 -0.092506892 -0.025193488 0.051911802 0.0964816725 0.077018815 -0.140898972 0.081642209 0.170304546 0.077900905 0.054145662 -0.097085512 0.223174180 -0.011135158 0.04921891
gs24 -0.06417467 -0.0149414733 -0.08825404 0.086663457 0.185635477 0.24803952 0.16026007 0.10322638 0.02203439 -0.086011354 -0.129393085 -0.07842642 0.05780942 -0.1641645916 -0.10844166 0.083523235 -0.005798852 0.049678102 0.157266164 -0.0530892790 -0.050186444 -0.029898637 -0.170267017 -0.203907801 0.055094962 0.151741113 -0.032774659 0.036993512 0.209782482 -0.25139183
gs25 0.04504363 -0.1477678435 0.06123978 0.030875101 0.006332271 -0.05142798 0.06244151 0.05938117 -0.05051385 0.102790865 0.009997114 -0.16018833 -0.16674864 0.0557757709 -0.02957331 0.007140476 -0.052433844 -0.019786407 -0.092644442 -0.0348063949 0.052160702 0.237650728 0.121105480 0.007749387 0.005139870 -0.067654482 -0.001748424 -0.080777781 0.146366359 -0.07803001
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> ## until the updated GSVAdata goes through the build system
> ## remove duplicated rows
> fnames <- featureNames(huangArrayRMAnoBatchCommon_eset)
> mask <- duplicated(fnames)
> huangArrayRMAnoBatchCommon_eset <- huangArrayRMAnoBatchCommon_eset[!mask, ]
> pickrellCountsArgonneCQNcommon_eset <- pickrellCountsArgonneCQNcommon_eset[!mask, ]
>
> 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)
> 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 -0.14230367 -0.315422586 -0.391252778 0.21314789 0.398273101 -0.02979645 0.17463104 0.267085366 0.197413154 0.07317030 0.0151842356 0.27511240 0.0810594643 -0.10663006 -0.191364179 -0.30618220 -0.25336772 -0.371841240 0.131350533 0.121203177 0.19187367 -0.453188679 -0.23038804 0.10202697 0.13430550 -0.007922221 0.16012876 -0.1026394845 -0.19874779 0.201905986 0.379079882 0.288111160 0.003129612 -0.36268779 0.109323303 0.25876115
KEGG_CITRATE_CYCLE_TCA_CYCLE -0.20050240 0.251659171 0.012907911 -0.23516857 0.167389776 -0.18868132 -0.09560810 0.023323070 0.253204612 -0.29805871 0.3431470095 0.11991763 0.1565766061 0.43928238 -0.115310950 -0.41021070 -0.51450945 0.101191356 0.022557303 0.212326603 -0.29059095 -0.366166646 0.19519820 0.34074454 -0.29218845 -0.137564423 -0.03874015 -0.0460878609 -0.15938696 -0.197978984 0.005781405 0.139048823 0.376558877 -0.11695718 0.398691360 0.08538487
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.13532736 -0.345433492 0.011710140 0.10461510 0.533833683 0.08497909 -0.07344553 0.339736015 0.185290991 -0.01914787 0.3436538099 0.15113342 0.0435975273 0.34068607 -0.320374734 -0.12343554 -0.52009025 -0.079637040 0.245999513 0.006539003 0.29725419 -0.494264566 -0.37543565 0.04379510 -0.10577650 -0.067638603 0.07219409 -0.1346995651 -0.28420602 -0.008962224 -0.009796505 0.408486750 -0.058106310 -0.20736744 0.134989826 0.33162025
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS -0.04674354 0.263195829 -0.247770620 -0.57095581 -0.151561771 -0.12045011 -0.22560104 0.154107744 0.171422759 -0.41538904 0.4061269795 0.32836635 -0.3398766485 0.45244001 0.238518510 -0.52846452 0.06897794 0.239050610 0.197501686 0.196563817 0.19246698 -0.281678574 -0.14631769 -0.07506140 -0.17403834 -0.357561908 0.19240461 0.4639167217 -0.30857693 0.066925762 0.107648843 -0.244720710 -0.001734512 -0.15569292 0.158727246 0.17601071
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM -0.05032619 -0.258191115 -0.272637165 0.02525198 0.465148979 -0.07264436 -0.08922090 0.179778439 0.176454883 0.08577523 0.1956641902 0.03330815 -0.0389123845 0.21832430 -0.058259416 -0.21799128 -0.41770899 -0.167326797 -0.116287665 0.028178393 0.18546795 -0.006915134 -0.35946143 0.04791420 0.12817416 0.320065055 0.14820768 -0.3569579979 -0.32557325 -0.201263232 0.257115785 0.243139572 0.180855314 0.04036292 0.077337949 0.11527875
KEGG_GALACTOSE_METABOLISM -0.50995845 -0.329079468 -0.339175575 0.17973234 0.589347614 -0.05162470 -0.02715106 0.011294677 0.114013797 0.20364017 0.0764356949 0.18293872 0.1712761979 0.09906587 -0.421107554 -0.30991624 -0.40972409 -0.552561906 0.134900019 0.312563354 0.40474331 -0.315001807 -0.45834570 0.24600213 0.36614165 -0.301648195 0.46863888 -0.1203792148 -0.47812544 -0.138757200 0.179735274 0.362123024 -0.116536784 -0.27757268 0.332831363 0.57291951
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.39703075 0.102716763 -0.055758439 0.31975221 0.117864410 -0.47757507 -0.27421719 0.489639438 -0.092044451 -0.05615840 -0.0733668926 -0.21507390 0.1917605063 0.31436950 0.036531537 0.05068651 0.06931287 -0.242851457 -0.076828096 -0.137640062 -0.70426332 -0.249548739 0.04489322 0.16341080 0.10221980 0.200025490 -0.62964039 -0.0648658968 -0.42547266 0.070369223 0.327559970 -0.007865333 0.202249029 0.02620757 -0.341097439 0.31102195
KEGG_FATTY_ACID_METABOLISM 0.03499557 0.183481630 0.209868940 -0.24526403 0.208740708 -0.11867729 -0.23905993 0.499149905 0.389621617 -0.20723774 0.1003775624 0.28752464 0.0264952630 0.13270380 -0.078963095 -0.35370866 -0.26220000 0.023136891 0.091846094 0.130728497 -0.32229224 -0.044506799 -0.17713704 0.13893632 -0.29212370 -0.120188772 -0.42197883 -0.1038247609 -0.09705027 -0.116454060 0.246489111 0.136899664 0.489237584 -0.07581183 0.016507828 0.03745853
KEGG_STEROID_BIOSYNTHESIS 0.20009807 -0.181590600 -0.495057872 -0.25999420 0.190318716 -0.32380418 0.40236927 0.555545362 0.335883859 -0.30628334 0.0994301550 0.02953368 -0.3429990844 0.33510274 0.482927930 -0.46774054 -0.41087983 0.363293352 -0.317192255 0.185389439 0.06846786 -0.460804383 -0.03811268 0.10386440 0.18840391 -0.277020767 -0.31775356 -0.3350533324 0.04572225 0.498123402 0.204400076 0.258186496 0.104633531 0.32977002 0.105979796 0.04778385
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS -0.22614949 0.327895536 -0.044963402 0.34520160 -0.324080107 -0.37005067 0.38061477 0.506003656 -0.277633599 -0.46620361 -0.3553865693 0.38408513 -0.1610969650 0.32344843 -0.391809219 -0.04010219 -0.34840499 0.440076802 -0.553451905 0.333395458 -0.41467805 0.088706867 0.11559089 0.49584759 -0.18691696 -0.289465112 -0.25327459 0.4882409667 0.48875862 0.684163843 0.405809338 -0.411231653 0.071450744 0.46791088 -0.051584981 -0.05530372
KEGG_STEROID_HORMONE_BIOSYNTHESIS 0.36671210 -0.044753334 -0.314703043 0.36116780 -0.116640526 -0.57441058 0.06518260 0.124107112 -0.153795570 -0.03460938 0.2548813094 -0.25833519 -0.1929012102 -0.01705796 0.005540414 0.20204739 0.07500285 -0.152295626 -0.175847740 0.169535820 -0.31054108 -0.288247072 -0.32233172 0.25541302 0.10269411 -0.242164220 -0.02773543 0.1147712590 0.20472937 0.091114751 0.444999725 0.138202887 -0.099910183 0.19770815 -0.322877108 0.38977634
KEGG_OXIDATIVE_PHOSPHORYLATION -0.44463189 0.405657198 0.315892634 -0.38462194 -0.063028804 0.20080896 -0.22585921 0.041829730 -0.078383761 -0.04923779 0.3668914393 -0.09328146 0.1964486364 0.31315273 -0.186534968 -0.36302054 -0.30193772 0.313561618 0.235744939 -0.322548387 -0.29735863 -0.198843886 -0.08765849 0.26407152 -0.24776804 0.241277903 0.12809953 -0.2093056215 -0.13991504 -0.165510760 0.004363026 0.173885611 0.285551064 -0.03747100 0.350960284 -0.14799876
KEGG_PURINE_METABOLISM -0.12429947 -0.003146735 0.109750349 0.02407314 0.152251724 0.20601792 0.04975895 0.087671238 -0.162044311 -0.08810469 0.2675309252 0.13421712 0.0005983356 0.19999998 -0.016663670 -0.19442126 -0.19597096 0.160113602 -0.004919668 -0.160288451 0.05043435 -0.238070609 -0.19697287 0.06490013 -0.20201793 0.064661415 -0.02823185 0.0008141729 -0.03520901 -0.008240455 0.054601543 -0.011461863 0.123583714 -0.14260536 0.001604703 -0.07538664
KEGG_PYRIMIDINE_METABOLISM -0.07969123 0.018479830 0.237335120 0.02680913 -0.007995819 0.25078444 -0.04171819 0.232922315 -0.155937293 -0.15883818 0.2909598842 0.19325236 -0.0970061662 0.19946686 0.037485420 -0.17798970 -0.14719367 0.256222265 0.019930009 -0.089948280 0.16264470 -0.308533382 -0.08200015 0.02988157 -0.30636924 0.090131040 -0.09054591 -0.1749494745 -0.09480720 -0.130857031 -0.040135166 -0.067286057 0.334271675 -0.05879758 -0.032964519 -0.17672172
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM -0.13064364 -0.065911721 -0.134222400 -0.15808267 0.026407189 -0.22107254 0.14077844 0.306640325 -0.123790795 -0.17620057 -0.1726825520 0.30252067 -0.0864643151 0.09958601 0.192126250 0.31442915 -0.31609967 -0.125684993 0.295597931 0.179207683 -0.20454937 0.057361897 -0.14883905 0.04965298 0.12243300 -0.041113555 -0.07917053 0.1816381096 -0.10277463 0.195475554 0.285753383 0.082372899 -0.370044975 -0.06073283 -0.243940084 0.22641916
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.10846488 -0.463507010 -0.180872151 0.09430933 0.244190256 -0.15405349 0.22393116 0.054212250 0.280540684 0.13649494 0.0599544061 -0.28868115 -0.0460531567 0.01265874 0.151929342 0.41789314 -0.13735320 -0.372284254 -0.406066496 0.282293938 0.19600499 -0.021052194 -0.26533358 0.12269137 0.26620757 0.058984278 0.05044338 -0.2505298486 -0.05301505 0.085669602 0.197644910 0.201488640 -0.407099059 -0.14256992 0.201256510 0.15101871
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.31330678 -0.149492749 0.003483417 0.19263550 -0.070024135 0.04076325 0.14227568 0.297635845 0.200688737 -0.18331111 0.2418556355 0.26735951 -0.2921105065 0.16958516 0.349104212 0.15204901 -0.22730835 -0.020102228 0.165816873 -0.283890575 0.23251096 -0.391190301 0.09379114 -0.22493866 -0.11044920 -0.372845225 -0.43902463 0.1716953214 0.03214754 0.168923799 -0.116190352 -0.006898610 -0.225469408 -0.18264898 0.214327770 -0.12475506
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.13821704 0.310127784 0.066445588 -0.42511864 -0.090306905 0.17837211 -0.19796655 0.347010789 0.408154036 -0.49673276 0.4127975060 0.22029835 0.2082638952 0.22095995 0.097006653 -0.28459992 -0.23839562 -0.180980405 0.227099410 0.266237949 -0.26309956 -0.366347365 -0.24746034 0.08971504 -0.26988765 -0.356087684 -0.48033192 0.2879096649 0.04729230 0.216578558 0.054749956 -0.098705529 0.327656315 -0.45815823 0.271899213 0.29958118
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.21234031 0.328164338 -0.305429769 -0.40920870 0.154270745 0.29337437 -0.24124926 -0.242270521 0.183690508 -0.57969585 0.4054083846 0.24857693 0.1309828553 0.50247869 0.270577765 0.03840523 -0.02241916 -0.145601032 0.137344238 0.442709981 0.39693964 -0.292615556 -0.12543161 -0.19155625 -0.07526516 -0.258038832 0.05263564 -0.2392736110 -0.27129310 -0.410804271 0.113044178 -0.264001250 -0.443467665 0.26368623 0.710107163 -0.01510618
KEGG_LYSINE_DEGRADATION -0.04858688 0.007615060 0.229421096 0.08925233 0.038306122 0.28980546 -0.18136349 0.186751148 0.202034280 -0.15545560 0.2126122092 0.16006097 0.2902420241 -0.09167494 0.074552004 -0.20477042 -0.11043819 -0.118851885 -0.043566480 0.235327437 0.07804014 -0.291097266 -0.01691432 -0.21943620 -0.20989917 0.076703134 -0.27596968 0.0388993077 -0.12327597 -0.055137936 -0.080184092 -0.017057734 0.003258048 -0.40132421 0.136618821 0.01103533
KEGG_ARGININE_AND_PROLINE_METABOLISM -0.22599881 0.046481159 -0.042679823 0.01685008 0.185540061 -0.31435358 0.33873171 0.146647899 -0.125142798 -0.04144693 -0.1308233076 -0.23631365 -0.0862667676 0.12265902 0.040207439 0.01955411 -0.23852570 -0.417826188 0.099780708 -0.025387365 0.06735798 0.061697207 -0.17988293 0.28098355 0.26353347 0.116707414 0.03351622 -0.2677372049 -0.11117794 0.309730283 0.208703010 0.293429518 -0.140256326 0.08662591 0.021626117 0.09297224
KEGG_HISTIDINE_METABOLISM 0.36509136 0.232658699 -0.116502900 -0.05141446 0.328105573 -0.20719131 -0.09511699 0.073873353 0.004448375 -0.21104151 -0.2754103889 -0.08738851 -0.2219436943 -0.04830135 0.222754115 0.07953853 0.10675039 0.008570392 -0.158305200 -0.207207830 -0.07062902 0.328890134 -0.03290924 -0.12579803 0.14889977 -0.369990857 -0.44130723 0.3027378486 -0.35216472 0.318584212 0.085706968 -0.328382753 0.058090870 -0.01746631 -0.141792587 -0.22080931
KEGG_TYROSINE_METABOLISM 0.20146600 0.168748206 -0.038021560 -0.19672569 -0.075048632 -0.12221566 0.33223135 -0.077860830 -0.191343952 -0.18419100 0.0009062282 -0.41370558 -0.1984151146 0.44633162 0.460112746 -0.23661823 0.06304089 0.446618130 -0.340634185 -0.263493921 0.32434436 0.147263398 -0.02495879 -0.16870285 -0.06053492 -0.228179608 -0.09131817 0.2054001200 -0.14089275 -0.124542842 0.280838580 -0.404680384 -0.005635066 0.41960567 0.045597099 -0.10641710
KEGG_PHENYLALANINE_METABOLISM 0.14987883 0.306094920 -0.425609638 0.03175427 0.007934090 -0.43992623 0.41671291 0.002250151 -0.664926010 0.33908117 -0.1346745613 -0.56306513 -0.3409626816 0.23351887 0.387413366 -0.14053193 -0.13915959 0.402187388 -0.060910823 0.196879226 0.30686970 -0.367733224 0.39944412 0.09814593 0.19222915 -0.451592015 0.02516237 0.4205597858 0.13969499 -0.168737298 0.038140347 -0.119329329 -0.453376906 0.58562092 0.154957006 -0.40567626
KEGG_TRYPTOPHAN_METABOLISM 0.02974690 0.069678200 0.164973394 -0.04936804 0.276382946 -0.39624538 -0.07475994 0.254781450 0.189667871 -0.16626755 -0.0767493207 0.10596150 -0.0679683568 0.10871564 -0.205792806 -0.07443261 -0.14722023 -0.200909073 0.338823015 0.029115397 -0.38027834 -0.188845048 0.04982826 -0.07708070 0.08733682 -0.026228617 -0.28185008 0.1056077412 -0.15419588 -0.065214119 0.059542190 -0.027720896 0.418277752 0.08051465 -0.197805216 0.01754684
> pickrellPar <- gsvaParam(pickrellCountsArgonneCQNcommon_eset,
+ canonicalC2BroadSets, minSize=5, maxSize=500,
+ kcdf="Poisson")
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
> 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 0.22812891 -0.263355222 -0.37470050 0.290732334 0.17079093 -0.45765232 0.50012601 -0.09532256 -0.47875336 0.2005760985 0.092621366 0.393690568 -0.10337215 0.25814796 -0.007047109 -0.32196546 0.54100312 0.36730644 -0.229340073 -0.21569337 -0.39089158 -0.10367966 -0.0265281455 0.206218417 -0.38405692 -0.26149665 0.11109491 -0.305540564 -0.23084358 0.119516674 0.40469862 -0.359303191 -0.2285660734 0.0670553834 -0.193418010 0.406591786
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.19353985 -0.200671800 -0.31936816 0.257300219 0.09459388 -0.14437972 0.58037080 0.22069982 -0.48416294 -0.0911133032 0.142997298 -0.013405272 0.21749563 0.14846560 0.331053799 -0.62290688 0.26557435 0.10178204 -0.243753239 -0.08360178 -0.13185028 -0.18973195 0.2221045889 -0.008182147 -0.27726362 -0.32679981 0.55375324 -0.272956015 -0.41562145 -0.238571669 0.23559980 -0.333287901 -0.4136149051 0.3504867977 -0.033474324 -0.001807616
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.39550501 -0.351321414 -0.14110425 0.358243057 0.16435766 -0.26645789 0.66763824 0.18030231 -0.55044204 0.0557952309 0.021388295 0.576276913 0.11071439 0.29896526 0.104972515 -0.50323751 0.57733745 0.46874390 -0.256221334 -0.36544895 -0.33575684 -0.39328574 0.1106353940 0.023796472 -0.34202930 -0.25875177 0.28102418 -0.433601675 -0.31440655 -0.006812749 0.26563946 -0.454982215 -0.4530852168 0.2943696221 -0.265834459 0.464109149
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.30352162 -0.233816407 -0.27160065 -0.246247207 -0.06071677 0.04536230 0.38822954 -0.15951208 0.02167093 -0.0009868643 0.156336200 -0.068057068 -0.26097473 0.47006050 0.358846550 -0.51169838 0.41369471 0.25978330 0.147722431 -0.10416667 0.29383289 -0.32583477 -0.3409895574 -0.079554856 -0.25840080 -0.55447175 0.33358642 0.470985307 -0.02891824 0.104965489 0.29526021 -0.142020689 0.3092595811 -0.0459739970 -0.268403065 0.119173232
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.11033580 -0.062206809 -0.04584560 0.442596321 -0.43860752 -0.26354440 0.47352638 0.10394622 -0.35492025 0.1683707621 0.143921586 0.214073587 0.15383886 0.01670041 0.220658935 -0.31831394 0.48932471 0.46125203 -0.425536886 -0.19921231 -0.31866404 0.01331120 -0.0384217078 -0.043444513 -0.35216375 -0.12959691 0.26961102 -0.288865569 -0.32149898 -0.241547259 0.35727062 -0.185325504 -0.3766633793 0.3981693832 -0.189099092 0.344009489
KEGG_GALACTOSE_METABOLISM 0.05968213 -0.423880642 -0.04004200 0.349477244 -0.12227027 -0.46339930 0.51695869 -0.01678146 -0.35296517 0.2445369055 0.472971320 0.344522701 0.33867856 0.24989655 0.250426294 -0.45236845 0.57775802 0.21524751 -0.336019746 -0.08788026 -0.42317686 -0.04080587 -0.2214574734 0.056153250 -0.07821159 0.07863864 0.27266698 -0.411791653 -0.36014334 -0.190298991 0.39452862 -0.533045360 -0.4125257996 0.3437504852 -0.176878763 0.513759918
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.51787543 0.042034908 -0.12451085 -0.038064187 0.31987038 -0.46521958 0.39708699 0.01144431 0.37686424 0.5270750790 -0.001858769 -0.116619796 -0.05921058 0.71771018 0.241435211 -0.28758375 0.69491752 0.45982511 0.297599608 -0.50769311 -0.41537974 -0.27260468 -0.0509472657 0.414217903 -0.23402892 -0.52793899 -0.51628394 0.447889841 -0.42312055 0.175658085 -0.07464253 0.344370366 0.2088021678 -0.3224188559 -0.391531733 0.285580764
KEGG_FATTY_ACID_METABOLISM 0.20823397 -0.241921084 -0.30379479 0.187014213 0.29338100 -0.08777247 0.52267768 0.27472038 -0.34093551 0.1468463154 0.062462542 0.085884109 0.13921725 0.51255637 0.291260701 -0.50392822 0.43325585 0.28246279 -0.303333035 -0.30577707 -0.18311108 -0.13226462 0.0150380402 0.283730125 -0.48304687 -0.50004910 0.09637623 -0.008330810 -0.31248520 0.240872277 0.20586330 -0.037848767 -0.3293889268 -0.0002619859 -0.139285035 0.340043918
KEGG_STEROID_BIOSYNTHESIS 0.33555025 0.080447197 -0.52654139 -0.264233483 0.32230491 0.07428098 0.30042368 0.29034851 -0.28507907 -0.6240119550 -0.150252031 -0.315794357 0.10365448 0.12635135 0.040393332 -0.37074397 -0.17108798 -0.02795860 -0.361857163 -0.33292803 -0.30373042 -0.19679981 0.6254377288 -0.009132700 0.19306085 0.09838023 0.13679885 -0.116683420 -0.26307803 -0.013155328 0.20258065 0.113702556 0.1627510357 0.5348554773 0.511929756 -0.189486235
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 0.15631681 0.084781957 -0.52932434 0.552990565 0.26301727 -0.59722302 0.12192049 0.47568307 0.39619228 -0.4647553926 -0.432516961 0.259251836 0.48663470 -0.03608670 -0.087762940 -0.40806006 -0.38975683 0.44392363 -0.215684354 -0.06839988 -0.20773783 0.30163867 0.2339610147 0.628355197 -0.21630584 -0.24968799 -0.29361770 0.204281767 0.38017089 0.372299022 0.35485746 0.166369614 -0.1046542740 -0.3541904396 -0.185978451 0.005576856
KEGG_STEROID_HORMONE_BIOSYNTHESIS 0.38401346 0.114401373 -0.45576082 0.356676495 -0.25638830 -0.29368341 -0.15897709 0.15045590 0.39649319 -0.0469501629 -0.117706482 -0.020320540 0.05344534 0.23711538 -0.066561132 0.25946951 0.10909131 -0.13089860 -0.209798086 -0.28930757 -0.15301440 0.38772282 -0.3239550451 0.274999683 0.25274925 0.01140588 -0.01957855 0.523475320 0.25999884 -0.202333818 0.14865078 0.497052412 -0.0003392273 -0.4017935592 -0.318178751 0.216543081
KEGG_OXIDATIVE_PHOSPHORYLATION 0.03275894 -0.066687128 -0.24411448 0.178976382 -0.07739081 0.23839051 0.53479936 0.11062943 -0.58614604 -0.1231529161 0.011086897 0.254776797 0.10757155 0.23088898 0.196978485 -0.21208191 0.13210528 0.22598485 -0.166527579 -0.12403773 0.02785705 -0.11083714 0.0482978612 -0.293151501 -0.43458192 -0.36542734 0.06548564 -0.307834152 0.24198224 -0.185694934 0.25245395 -0.015265711 -0.1000535768 0.2486890645 -0.322154550 -0.196467278
KEGG_PURINE_METABOLISM 0.20023659 -0.107367072 -0.10728443 0.291663773 -0.05283553 -0.02859522 0.36157660 0.19316332 -0.19143021 -0.1572998000 0.049080483 0.109067828 -0.11833371 0.10564365 0.139338503 -0.10233547 0.24853991 0.18038953 0.046367008 -0.21468925 -0.19907099 -0.17785664 -0.1297500619 -0.149496262 -0.20375506 -0.18721379 0.14549532 -0.025164874 0.03659184 0.032750693 -0.01289068 0.002391921 -0.1715995805 0.1037162394 -0.157361053 -0.016062020
KEGG_PYRIMIDINE_METABOLISM 0.31160686 -0.314337137 0.02465540 0.453228985 -0.07810397 0.12015916 0.43909081 0.15814096 -0.34017799 -0.0081584730 0.044825193 0.110742509 -0.26372825 0.22189578 0.248993194 -0.26563543 0.21792676 0.26036321 -0.170161658 -0.24625352 -0.26111910 -0.28286211 -0.0132632619 -0.175035994 -0.39042012 -0.27213628 0.21360327 0.007963696 0.07924093 0.141929379 -0.08314588 0.091267966 -0.2759966513 0.3117578458 -0.421748951 0.011205471
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.04137278 0.243239788 -0.16090629 0.042626922 0.40716099 0.02795095 0.08519888 0.08165140 -0.05544785 -0.2042398482 -0.079047867 -0.304524860 -0.03288761 0.11420844 0.310266126 -0.16555921 0.02341918 0.02665627 0.080941061 -0.12399840 0.09060201 0.03870403 -0.2568792442 0.215932167 -0.26034017 -0.15336446 0.26947058 0.342014672 -0.28436268 0.223771668 -0.05678723 0.114388282 -0.0220268977 -0.3108220646 0.129566526 0.237023883
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.24286149 -0.281021942 -0.11196471 0.119410270 0.17458480 -0.21600024 -0.30947266 -0.11270084 0.31554246 -0.1544698212 -0.174652441 0.009889643 -0.39356493 0.15198519 0.304577250 -0.01314328 0.02626527 -0.23588917 0.195167717 -0.14020907 -0.14552128 0.28081761 -0.0969045615 0.295113478 0.20735687 -0.09096551 0.19877101 -0.140658529 -0.05967062 0.530244229 -0.29150989 -0.018469164 -0.0648473323 -0.3563706157 0.352493400 0.245123799
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.46859153 -0.379300667 -0.01868216 0.429301488 0.17347937 -0.20479501 0.30306957 0.34379252 -0.38026186 0.0857333714 -0.259806130 -0.051601632 -0.18492935 0.51260419 0.190312676 -0.43573176 0.26676090 -0.04452266 0.005188443 -0.49904874 -0.19476281 -0.04975948 -0.1802249032 -0.187156160 -0.11882846 -0.27860347 0.06497422 0.015459913 -0.26962268 0.396055231 -0.20336841 -0.056566339 -0.2623303556 0.0218337313 -0.149172969 0.296738232
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.13165312 -0.333486357 -0.25807014 0.212746862 0.16537668 -0.28578872 0.55522995 -0.12541421 -0.32444915 -0.0908361898 0.374830896 -0.059743969 0.18262115 0.52189107 0.300491230 -0.43227506 0.36348022 0.23608991 -0.251607492 -0.24494595 -0.23020864 -0.30715338 -0.1097869254 0.335750429 -0.42776978 -0.35468076 0.05586066 -0.011469915 -0.38304181 0.190347530 0.32810277 -0.106020282 -0.2278552818 -0.0010987744 -0.009598621 0.282065377
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.34866653 -0.129961799 -0.53134605 0.413981718 0.45007503 0.07242446 0.26567130 -0.21208186 -0.37406279 -0.6432922517 0.073564590 -0.169707405 -0.19330715 0.44350590 0.326741959 -0.39438102 0.20225333 -0.22872589 -0.344279983 0.21730971 -0.03203297 -0.33343673 -0.5599649471 0.105459222 -0.11361999 -0.25714223 0.53274773 -0.177539040 -0.15373291 0.311023102 0.28440312 -0.550490532 -0.2161631449 -0.1390562905 0.142388873 0.096096749
KEGG_LYSINE_DEGRADATION 0.18494876 -0.301470123 0.14132481 -0.002621688 0.05015042 0.13622957 0.33458090 0.17109948 -0.15867468 0.0003849763 0.054067800 -0.068680732 0.19042998 0.06804951 0.394760575 -0.30703160 0.06853304 -0.30397621 0.175905945 -0.20687387 -0.14129301 -0.10296603 0.1433435814 0.077433293 -0.18303745 -0.05981301 0.15445734 -0.069524038 -0.26483337 -0.115915730 0.01319768 -0.195524378 -0.3691190823 0.0982540134 0.020016829 0.173412122
KEGG_ARGININE_AND_PROLINE_METABOLISM 0.27313717 -0.006275212 -0.20431253 0.190536329 0.26357364 -0.08986962 0.33535841 0.08369295 -0.15741845 -0.0368390006 -0.011551509 -0.200019910 0.06866612 0.30451139 0.104228306 -0.29137253 0.28990804 0.07934982 0.006305633 -0.25713144 -0.29690035 0.17278938 -0.1979099576 0.243229750 -0.25100313 -0.11679394 0.11797791 0.054808974 -0.24014345 0.340464431 0.03801927 0.119241532 -0.1700499696 -0.1940067222 -0.059602030 0.053208863
KEGG_HISTIDINE_METABOLISM 0.32853038 -0.057164812 0.23315460 0.169742425 0.01570033 0.04234044 0.14603217 -0.18993749 0.10651264 0.0512641019 -0.228100268 -0.127091012 -0.23913329 0.17260826 0.063898693 -0.07849663 0.35259850 0.03083913 0.086876963 -0.09798041 -0.25217403 0.15586151 0.0460886670 0.127022739 -0.15770660 -0.39737625 -0.45113673 0.435864620 -0.03705763 0.051361970 -0.09271126 0.345100659 0.0779934347 0.1202706083 0.115079486 -0.106774127
KEGG_TYROSINE_METABOLISM -0.01145121 -0.195656442 -0.32679481 0.236210111 -0.23229989 0.20153868 0.22237215 0.26727784 -0.23845151 0.1921011166 -0.246175280 -0.118369345 -0.42849368 0.01975597 0.004091731 0.01083809 0.38756357 0.09763915 -0.181393091 0.19996544 0.41059691 0.05418104 -0.3215846275 0.182779499 -0.31116026 -0.45651782 0.33597072 0.131423856 0.29692628 -0.170172936 0.15571905 -0.081966569 0.2428263666 -0.0315041493 0.085376038 0.152931026
KEGG_PHENYLALANINE_METABOLISM 0.17876930 0.461533646 -0.62066204 -0.141533765 0.27696353 -0.20615287 -0.26584090 0.10882765 -0.12564179 -0.1941277338 -0.595634193 -0.090748269 -0.46544720 -0.44323209 -0.094230783 0.28219191 0.09985828 -0.08156841 0.487792811 -0.06706930 0.37972732 0.56110203 -0.1060520245 0.467821351 -0.17722929 -0.17697362 0.14854319 0.651027624 0.19579886 -0.289555438 -0.55517146 0.450858905 0.3373233877 0.1943208483 -0.124553187 -0.095947712
KEGG_TRYPTOPHAN_METABOLISM 0.02561159 0.043980374 -0.31897262 0.096835151 0.12979176 -0.18708412 0.21234061 0.05343963 0.09277264 -0.1502765995 0.007712090 0.065525644 0.14490981 0.31042699 0.208687246 -0.12850955 0.16001678 -0.11682337 0.159732707 -0.40441996 -0.29936947 0.20875791 -0.0002505521 0.127602204 -0.15109245 -0.26472714 -0.09219912 0.332216918 -0.29296983 0.016344873 -0.06296213 0.330906743 0.0411330692 -0.0550424496 -0.007991669 -0.070061618
>
> 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)
> 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 Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences"
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>
> ## 2024-10-25 regression test script for method PLAGE
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2024-10-25)
> 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 1.1025783 -0.9348073 1.2604604 -0.5213579 -0.1449497
g2 1.1178965 -1.1697762 -0.6188039 -1.5167080 -1.1104456
g3 -1.8181019 -1.1516529 0.9891236 -1.0173901 0.7009874
g4 -0.1944140 -0.3479166 -0.7471371 -0.6796938 1.5027270
g5 -0.6131956 1.0524922 -0.5313147 0.6119898 0.3619898
> 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 0.02447838 0.043046819 0.022861848 -0.205589482 0.296269175 -0.067897934 0.009365443 0.19588312 -0.0684628168 -0.291617125 -0.063006870 -0.11455848 0.08835384 -0.119133572 -0.37601451 -0.102001438 0.151576730 0.152276226 0.15277975 0.25092452 0.19334987 -0.098915077 -0.0001005365 0.24888404 -0.497851166 0.150840271 -0.002741001 -0.12972034 0.04674573 0.1099745959
gs2 -0.10178568 -0.053472411 0.071479021 -0.093621219 -0.072399323 -0.103159677 -0.062034022 0.02721190 0.1819690513 -0.287777155 -0.126437392 -0.35887078 -0.20239815 -0.121495901 -0.03866555 0.064362229 0.166928582 -0.026863222 0.12705474 0.30829495 0.15750072 0.002268741 0.3041365296 0.11596916 0.139708907 0.192069874 0.039868384 0.32833076 -0.40503919 -0.1731338719
gs3 0.17779308 0.071592632 0.270620060 -0.077277095 -0.019302111 0.126868806 -0.086853987 -0.30307648 -0.0348298803 -0.019370354 0.227896312 0.23609166 -0.09032615 -0.013311272 -0.34826436 -0.029041484 -0.099557829 0.300892267 -0.31844768 -0.30675683 -0.08269703 0.284752704 -0.0291969122 0.01426100 0.190455670 -0.030588916 0.265123514 -0.17290031 -0.07048839 -0.0340606277
gs4 0.25759609 -0.254492982 0.080978642 -0.004055315 -0.086043065 -0.123417896 -0.288733315 -0.32718323 0.0411331981 0.007359673 0.008524736 0.24000875 -0.07630829 0.229103183 0.22235742 -0.365661917 0.043984865 -0.073877606 -0.34461348 0.04982544 -0.08270833 -0.014992074 0.0473369465 0.24598765 0.255137779 -0.142763795 0.121315135 0.02014199 0.15747656 0.1565832421
gs5 -0.26658305 0.009191479 0.045889747 0.075042418 -0.120813297 -0.062880126 -0.040188276 0.03381215 0.1208426701 0.004976237 -0.134095694 -0.09329212 0.30211661 -0.122571093 0.05273484 -0.371743383 -0.247706938 0.002038086 0.29514483 0.02041488 -0.06849236 0.152934966 -0.4443875326 0.00769790 0.161935175 0.307711491 -0.086297751 0.05087519 0.30624209 0.1094508594
gs6 -0.02967177 -0.167833355 0.289639169 0.171349514 -0.199192094 -0.034608339 -0.053147572 0.09932621 0.0486712530 -0.135485792 -0.167373078 0.20786072 -0.33543358 0.261729235 -0.06337528 0.117558325 0.180279193 0.134357876 0.06623578 -0.46993983 -0.03262374 0.030706467 0.1863916489 -0.15054746 0.218410325 -0.176851183 -0.108836097 -0.19723796 0.17018022 0.1394611880
gs7 0.06538196 0.007432305 0.258760091 -0.104534416 -0.346284679 0.072286001 0.028237794 0.06264737 -0.0156785291 0.114503198 0.019159040 0.11848999 0.07722598 0.014076423 -0.45087879 0.199171795 -0.018874887 0.101164877 0.03287298 -0.11884208 -0.20324623 -0.135966627 0.0276708906 0.23704387 0.328593056 0.058186201 -0.189610917 -0.31026090 -0.21172824 0.2830024649
gs8 -0.04471483 0.172986335 0.103787622 -0.164001895 -0.037459650 0.092457117 0.162892740 0.14381823 -0.1461787896 -0.246417195 -0.310888852 0.13345676 -0.16485124 0.113211707 0.13035710 0.009277538 0.092433874 -0.050227616 -0.34590015 -0.24184945 0.27335602 0.141301229 -0.0091696602 0.08022849 0.088969419 0.022258268 0.091602557 0.40422755 -0.36259688 -0.1323663474
gs9 -0.11944724 0.143533850 0.351823913 0.281749543 0.198390812 0.057307528 -0.076415596 -0.10195476 0.1535173134 0.057941345 0.071707889 0.12465272 -0.08919620 -0.006817202 -0.06752316 0.056520726 0.289610117 -0.369075031 -0.42083899 -0.03580491 0.08108218 -0.102899050 -0.1040948672 -0.04314018 0.079397874 -0.012166255 -0.060546099 -0.07493752 0.15274445 -0.4151232048
gs10 -0.15529715 0.005162712 -0.028926887 0.130662355 -0.087438758 -0.024788523 -0.290780953 0.16304817 -0.0810228399 0.183361638 0.039224304 0.20150615 0.21417513 0.024292006 -0.42727473 0.149104384 0.077462575 -0.093852915 0.09365958 -0.25588015 0.42551010 0.328883017 -0.0340746265 -0.02042362 0.077556283 -0.062637805 -0.035462570 -0.11052027 -0.30158378 -0.1036428328
gs11 0.23088452 0.258497448 0.002121933 -0.049664145 0.001799611 -0.342971396 0.069584130 -0.03977552 -0.0947238405 0.344258219 0.233211300 0.04628435 0.25530317 0.055954286 0.10390439 -0.259182078 0.036701852 0.016139312 0.38211295 -0.18287088 -0.02022866 0.002056655 -0.2150096413 -0.05113764 -0.131168044 -0.027890511 -0.167723678 -0.37377799 -0.08309068 0.0004005619
gs12 0.36893428 0.079905973 0.340062195 0.066863523 -0.001375275 -0.201747508 -0.104603272 0.22967303 -0.0099144267 0.086249826 0.033231413 -0.20350438 -0.26581070 -0.126610894 -0.07890703 0.039609412 -0.236046132 0.356868041 -0.05948439 0.25194469 -0.09717973 -0.270028710 0.0706232327 0.12065834 -0.131516483 -0.025991581 -0.228226513 -0.06280950 -0.14466348 0.2037960457
gs13 0.04727186 -0.340485255 0.023224082 -0.164753838 0.016516900 -0.001777901 -0.187361910 0.01740602 -0.0001094913 -0.063010367 0.112667035 0.18847727 -0.14946861 0.265220611 0.06406449 0.205488606 -0.010818564 -0.270164606 0.02477045 -0.03068784 -0.05168573 -0.448712272 0.3925820069 0.10089206 -0.248927013 0.335926297 0.047563504 0.01356124 0.07522258 0.0371083991
gs14 0.09171102 -0.171087349 0.005961407 -0.129583198 0.113920225 0.184729880 -0.274669986 0.23527586 0.0464388232 0.189221179 -0.502011244 -0.08993939 -0.26693583 -0.040715119 0.16456834 0.182890884 0.001042862 0.195887248 0.14586565 0.26846729 -0.02004213 -0.186220595 0.2257239743 -0.29511563 -0.092364201 0.002637807 0.016553063 -0.05005107 -0.07295463 0.1207948643
gs15 0.07634385 0.118368763 -0.099520652 -0.156485377 0.432159040 -0.011977240 -0.046455409 0.31878830 -0.2495388558 -0.149853525 -0.327562453 -0.03271645 0.03896620 0.045648817 -0.08647621 -0.229077260 -0.126374888 0.258446375 0.43345552 0.12046262 -0.06747107 0.110845165 -0.0414678129 -0.13807531 -0.187459433 0.123690540 0.084855497 -0.10719499 -0.07532136 -0.0290023942
gs16 0.12352257 0.298895678 0.213586773 -0.030114679 -0.465236983 0.065941698 -0.094216862 0.20708549 0.1836981960 0.212471487 0.148857223 -0.05355188 -0.01907482 -0.077414161 0.04016011 0.066259373 -0.032663719 -0.027471649 -0.22132103 0.22093303 -0.02784611 -0.292466345 0.0911696464 -0.13567821 -0.305194028 -0.320655452 0.030416678 -0.08586795 0.17682026 0.1089556704
gs17 0.13633401 0.318461975 0.219676234 -0.165815112 0.137342478 -0.049518302 -0.032508924 -0.06929131 -0.0871331049 -0.042482482 -0.254647083 -0.06819946 0.11956909 -0.184365981 0.01299991 -0.121517638 0.015057311 -0.194170132 0.18633954 0.08787421 0.29702839 -0.033349595 -0.0776942581 0.35614443 0.183229388 -0.307159319 0.126675418 -0.40201676 -0.15607894 0.0492160048
gs18 0.11360883 0.111438426 -0.199205474 0.106139229 0.170763812 -0.210106656 -0.051706784 -0.15542186 -0.3053693182 0.290212170 -0.135708957 0.02463469 -0.07307542 0.376218686 -0.32815712 0.022559915 0.242895522 -0.008822336 -0.25722363 -0.18862209 0.11888541 0.024744135 -0.2000649472 0.01614921 0.169758696 -0.163748752 0.225965370 0.07532849 0.20829192 -0.0203611829
gs19 0.01845058 -0.120365114 -0.103874491 -0.228830086 0.253724933 0.077895903 -0.121451838 0.24679841 0.0001807351 -0.065887418 -0.170879049 -0.11422022 -0.08724724 0.338915690 0.25376709 0.056162099 0.031751360 -0.414193147 0.24742882 -0.14334209 0.12057683 0.236529048 0.2129691546 -0.14660144 -0.188974531 -0.132026661 -0.036956290 0.10376768 0.13117861 -0.2552473414
gs20 0.07128023 0.018467358 0.052481390 0.265863113 0.043212987 -0.056816513 0.194505304 0.23149839 -0.0023934571 0.074636697 0.037605016 -0.07069323 -0.15947090 -0.208295030 0.27531238 -0.519563814 -0.084127981 -0.131882130 0.35520242 -0.04169831 0.08530119 -0.075583180 0.0496430166 -0.19536989 0.071516672 0.043650968 -0.392705247 0.03382071 0.13790609 -0.1033042508
gs21 0.18877192 -0.022088696 0.260353844 0.176790992 -0.018579467 0.062079204 0.289214399 -0.16910368 -0.2497252979 0.164906974 -0.491707494 0.18405417 -0.26993115 0.081841714 0.03421348 0.056164184 0.022498457 0.061503901 -0.15139219 -0.01383544 0.37179062 -0.110470711 -0.0555358113 -0.12727189 -0.135136397 -0.205386394 -0.011206727 -0.13074280 0.14208606 0.0658442144
gs22 0.12980968 0.038529275 0.078576873 -0.150466003 -0.418114234 -0.077967274 0.274468079 -0.21587548 0.1188294253 -0.151277321 -0.126438033 0.31171151 0.03860523 -0.047506636 0.02277296 -0.009837726 0.098509974 -0.064647855 0.19830267 0.32077994 0.08647237 -0.276440858 0.1124854866 -0.34499168 -0.004149448 0.205144641 -0.010498754 0.15049723 -0.23770297 -0.0495810663
gs23 -0.11885694 0.125013623 0.007422040 -0.188254347 -0.066766414 -0.121967871 -0.288255173 0.01322254 0.0078782741 -0.066308746 -0.111004738 -0.36597209 -0.13538603 -0.020222023 0.02176413 -0.262796632 0.179692301 0.142767656 0.41444912 0.27311595 0.31217249 0.082556722 0.1531863656 0.23473468 0.147487461 -0.016709046 -0.195189765 -0.09330736 -0.17432184 0.1098556593
gs24 0.14995687 -0.133502473 0.229492801 0.264852172 -0.294768810 -0.312707811 -0.026927911 -0.01536772 0.0133273369 0.151819521 -0.216093119 0.28462634 0.16670812 -0.349244646 -0.24218370 -0.091332782 -0.115233721 0.026882150 -0.15958877 0.19975923 0.03783832 -0.036498682 -0.0599659576 0.34027785 0.019912567 -0.059571406 -0.136965751 0.20728660 0.03391978 0.1232936031
gs25 -0.09232287 -0.097087022 -0.137010912 -0.049216910 0.047317795 0.448706474 -0.005560789 -0.13410384 -0.3816987680 -0.277767839 -0.246852220 0.07408401 0.03022269 0.222615075 0.02328394 -0.110521548 0.202986826 0.141392838 -0.26453802 0.12746162 -0.21289484 -0.038046246 -0.1030360136 0.07468120 0.017414752 0.240163493 -0.001822979 0.12683330 0.31389759 0.0614192179
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> ## until the updated GSVAdata goes through the build system
> ## remove duplicated rows
> fnames <- featureNames(huangArrayRMAnoBatchCommon_eset)
> mask <- duplicated(fnames)
> huangArrayRMAnoBatchCommon_eset <- huangArrayRMAnoBatchCommon_eset[!mask, ]
> pickrellCountsArgonneCQNcommon_eset <- pickrellCountsArgonneCQNcommon_eset[!mask, ]
>
> 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)
> 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)
> 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)
> 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
35.424 1.582 36.997
GSVA.Rcheck/tests/test_plage_newapi.Rout.save
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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>
> ## 2024-10-25 regression test script for method PLAGE
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2024-10-25)
> 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 1.1025783 -0.9348073 1.2604604 -0.5213579 -0.1449497
g2 1.1178965 -1.1697762 -0.6188039 -1.5167080 -1.1104456
g3 -1.8181019 -1.1516529 0.9891236 -1.0173901 0.7009874
g4 -0.1944140 -0.3479166 -0.7471371 -0.6796938 1.5027270
g5 -0.6131956 1.0524922 -0.5313147 0.6119898 0.3619898
> 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 0.02447838 0.043046819 0.022861848 -0.205589482 0.296269175 -0.067897934 0.009365443 0.19588312 -0.0684628168 -0.291617125 -0.063006870 -0.11455848 0.08835384 -0.119133572 -0.37601451 -0.102001438 0.151576730 0.152276226 0.15277975 0.25092452 0.19334987 -0.098915077 -0.0001005365 0.24888404 -0.497851166 0.150840271 -0.002741001 -0.12972034 0.04674573 0.1099745959
gs2 -0.10178568 -0.053472411 0.071479021 -0.093621219 -0.072399323 -0.103159677 -0.062034022 0.02721190 0.1819690513 -0.287777155 -0.126437392 -0.35887078 -0.20239815 -0.121495901 -0.03866555 0.064362229 0.166928582 -0.026863222 0.12705474 0.30829495 0.15750072 0.002268741 0.3041365296 0.11596916 0.139708907 0.192069874 0.039868384 0.32833076 -0.40503919 -0.1731338719
gs3 0.17779308 0.071592632 0.270620060 -0.077277095 -0.019302111 0.126868806 -0.086853987 -0.30307648 -0.0348298803 -0.019370354 0.227896312 0.23609166 -0.09032615 -0.013311272 -0.34826436 -0.029041484 -0.099557829 0.300892267 -0.31844768 -0.30675683 -0.08269703 0.284752704 -0.0291969122 0.01426100 0.190455670 -0.030588916 0.265123514 -0.17290031 -0.07048839 -0.0340606277
gs4 0.25759609 -0.254492982 0.080978642 -0.004055315 -0.086043065 -0.123417896 -0.288733315 -0.32718323 0.0411331981 0.007359673 0.008524736 0.24000875 -0.07630829 0.229103183 0.22235742 -0.365661917 0.043984865 -0.073877606 -0.34461348 0.04982544 -0.08270833 -0.014992074 0.0473369465 0.24598765 0.255137779 -0.142763795 0.121315135 0.02014199 0.15747656 0.1565832421
gs5 -0.26658305 0.009191479 0.045889747 0.075042418 -0.120813297 -0.062880126 -0.040188276 0.03381215 0.1208426701 0.004976237 -0.134095694 -0.09329212 0.30211661 -0.122571093 0.05273484 -0.371743383 -0.247706938 0.002038086 0.29514483 0.02041488 -0.06849236 0.152934966 -0.4443875326 0.00769790 0.161935175 0.307711491 -0.086297751 0.05087519 0.30624209 0.1094508594
gs6 -0.02967177 -0.167833355 0.289639169 0.171349514 -0.199192094 -0.034608339 -0.053147572 0.09932621 0.0486712530 -0.135485792 -0.167373078 0.20786072 -0.33543358 0.261729235 -0.06337528 0.117558325 0.180279193 0.134357876 0.06623578 -0.46993983 -0.03262374 0.030706467 0.1863916489 -0.15054746 0.218410325 -0.176851183 -0.108836097 -0.19723796 0.17018022 0.1394611880
gs7 0.06538196 0.007432305 0.258760091 -0.104534416 -0.346284679 0.072286001 0.028237794 0.06264737 -0.0156785291 0.114503198 0.019159040 0.11848999 0.07722598 0.014076423 -0.45087879 0.199171795 -0.018874887 0.101164877 0.03287298 -0.11884208 -0.20324623 -0.135966627 0.0276708906 0.23704387 0.328593056 0.058186201 -0.189610917 -0.31026090 -0.21172824 0.2830024649
gs8 -0.04471483 0.172986335 0.103787622 -0.164001895 -0.037459650 0.092457117 0.162892740 0.14381823 -0.1461787896 -0.246417195 -0.310888852 0.13345676 -0.16485124 0.113211707 0.13035710 0.009277538 0.092433874 -0.050227616 -0.34590015 -0.24184945 0.27335602 0.141301229 -0.0091696602 0.08022849 0.088969419 0.022258268 0.091602557 0.40422755 -0.36259688 -0.1323663474
gs9 -0.11944724 0.143533850 0.351823913 0.281749543 0.198390812 0.057307528 -0.076415596 -0.10195476 0.1535173134 0.057941345 0.071707889 0.12465272 -0.08919620 -0.006817202 -0.06752316 0.056520726 0.289610117 -0.369075031 -0.42083899 -0.03580491 0.08108218 -0.102899050 -0.1040948672 -0.04314018 0.079397874 -0.012166255 -0.060546099 -0.07493752 0.15274445 -0.4151232048
gs10 -0.15529715 0.005162712 -0.028926887 0.130662355 -0.087438758 -0.024788523 -0.290780953 0.16304817 -0.0810228399 0.183361638 0.039224304 0.20150615 0.21417513 0.024292006 -0.42727473 0.149104384 0.077462575 -0.093852915 0.09365958 -0.25588015 0.42551010 0.328883017 -0.0340746265 -0.02042362 0.077556283 -0.062637805 -0.035462570 -0.11052027 -0.30158378 -0.1036428328
gs11 0.23088452 0.258497448 0.002121933 -0.049664145 0.001799611 -0.342971396 0.069584130 -0.03977552 -0.0947238405 0.344258219 0.233211300 0.04628435 0.25530317 0.055954286 0.10390439 -0.259182078 0.036701852 0.016139312 0.38211295 -0.18287088 -0.02022866 0.002056655 -0.2150096413 -0.05113764 -0.131168044 -0.027890511 -0.167723678 -0.37377799 -0.08309068 0.0004005619
gs12 0.36893428 0.079905973 0.340062195 0.066863523 -0.001375275 -0.201747508 -0.104603272 0.22967303 -0.0099144267 0.086249826 0.033231413 -0.20350438 -0.26581070 -0.126610894 -0.07890703 0.039609412 -0.236046132 0.356868041 -0.05948439 0.25194469 -0.09717973 -0.270028710 0.0706232327 0.12065834 -0.131516483 -0.025991581 -0.228226513 -0.06280950 -0.14466348 0.2037960457
gs13 0.04727186 -0.340485255 0.023224082 -0.164753838 0.016516900 -0.001777901 -0.187361910 0.01740602 -0.0001094913 -0.063010367 0.112667035 0.18847727 -0.14946861 0.265220611 0.06406449 0.205488606 -0.010818564 -0.270164606 0.02477045 -0.03068784 -0.05168573 -0.448712272 0.3925820069 0.10089206 -0.248927013 0.335926297 0.047563504 0.01356124 0.07522258 0.0371083991
gs14 0.09171102 -0.171087349 0.005961407 -0.129583198 0.113920225 0.184729880 -0.274669986 0.23527586 0.0464388232 0.189221179 -0.502011244 -0.08993939 -0.26693583 -0.040715119 0.16456834 0.182890884 0.001042862 0.195887248 0.14586565 0.26846729 -0.02004213 -0.186220595 0.2257239743 -0.29511563 -0.092364201 0.002637807 0.016553063 -0.05005107 -0.07295463 0.1207948643
gs15 0.07634385 0.118368763 -0.099520652 -0.156485377 0.432159040 -0.011977240 -0.046455409 0.31878830 -0.2495388558 -0.149853525 -0.327562453 -0.03271645 0.03896620 0.045648817 -0.08647621 -0.229077260 -0.126374888 0.258446375 0.43345552 0.12046262 -0.06747107 0.110845165 -0.0414678129 -0.13807531 -0.187459433 0.123690540 0.084855497 -0.10719499 -0.07532136 -0.0290023942
gs16 0.12352257 0.298895678 0.213586773 -0.030114679 -0.465236983 0.065941698 -0.094216862 0.20708549 0.1836981960 0.212471487 0.148857223 -0.05355188 -0.01907482 -0.077414161 0.04016011 0.066259373 -0.032663719 -0.027471649 -0.22132103 0.22093303 -0.02784611 -0.292466345 0.0911696464 -0.13567821 -0.305194028 -0.320655452 0.030416678 -0.08586795 0.17682026 0.1089556704
gs17 0.13633401 0.318461975 0.219676234 -0.165815112 0.137342478 -0.049518302 -0.032508924 -0.06929131 -0.0871331049 -0.042482482 -0.254647083 -0.06819946 0.11956909 -0.184365981 0.01299991 -0.121517638 0.015057311 -0.194170132 0.18633954 0.08787421 0.29702839 -0.033349595 -0.0776942581 0.35614443 0.183229388 -0.307159319 0.126675418 -0.40201676 -0.15607894 0.0492160048
gs18 0.11360883 0.111438426 -0.199205474 0.106139229 0.170763812 -0.210106656 -0.051706784 -0.15542186 -0.3053693182 0.290212170 -0.135708957 0.02463469 -0.07307542 0.376218686 -0.32815712 0.022559915 0.242895522 -0.008822336 -0.25722363 -0.18862209 0.11888541 0.024744135 -0.2000649472 0.01614921 0.169758696 -0.163748752 0.225965370 0.07532849 0.20829192 -0.0203611829
gs19 0.01845058 -0.120365114 -0.103874491 -0.228830086 0.253724933 0.077895903 -0.121451838 0.24679841 0.0001807351 -0.065887418 -0.170879049 -0.11422022 -0.08724724 0.338915690 0.25376709 0.056162099 0.031751360 -0.414193147 0.24742882 -0.14334209 0.12057683 0.236529048 0.2129691546 -0.14660144 -0.188974531 -0.132026661 -0.036956290 0.10376768 0.13117861 -0.2552473414
gs20 0.07128023 0.018467358 0.052481390 0.265863113 0.043212987 -0.056816513 0.194505304 0.23149839 -0.0023934571 0.074636697 0.037605016 -0.07069323 -0.15947090 -0.208295030 0.27531238 -0.519563814 -0.084127981 -0.131882130 0.35520242 -0.04169831 0.08530119 -0.075583180 0.0496430166 -0.19536989 0.071516672 0.043650968 -0.392705247 0.03382071 0.13790609 -0.1033042508
gs21 0.18877192 -0.022088696 0.260353844 0.176790992 -0.018579467 0.062079204 0.289214399 -0.16910368 -0.2497252979 0.164906974 -0.491707494 0.18405417 -0.26993115 0.081841714 0.03421348 0.056164184 0.022498457 0.061503901 -0.15139219 -0.01383544 0.37179062 -0.110470711 -0.0555358113 -0.12727189 -0.135136397 -0.205386394 -0.011206727 -0.13074280 0.14208606 0.0658442144
gs22 0.12980968 0.038529275 0.078576873 -0.150466003 -0.418114234 -0.077967274 0.274468079 -0.21587548 0.1188294253 -0.151277321 -0.126438033 0.31171151 0.03860523 -0.047506636 0.02277296 -0.009837726 0.098509974 -0.064647855 0.19830267 0.32077994 0.08647237 -0.276440858 0.1124854866 -0.34499168 -0.004149448 0.205144641 -0.010498754 0.15049723 -0.23770297 -0.0495810663
gs23 -0.11885694 0.125013623 0.007422040 -0.188254347 -0.066766414 -0.121967871 -0.288255173 0.01322254 0.0078782741 -0.066308746 -0.111004738 -0.36597209 -0.13538603 -0.020222023 0.02176413 -0.262796632 0.179692301 0.142767656 0.41444912 0.27311595 0.31217249 0.082556722 0.1531863656 0.23473468 0.147487461 -0.016709046 -0.195189765 -0.09330736 -0.17432184 0.1098556593
gs24 0.14995687 -0.133502473 0.229492801 0.264852172 -0.294768810 -0.312707811 -0.026927911 -0.01536772 0.0133273369 0.151819521 -0.216093119 0.28462634 0.16670812 -0.349244646 -0.24218370 -0.091332782 -0.115233721 0.026882150 -0.15958877 0.19975923 0.03783832 -0.036498682 -0.0599659576 0.34027785 0.019912567 -0.059571406 -0.136965751 0.20728660 0.03391978 0.1232936031
gs25 -0.09232287 -0.097087022 -0.137010912 -0.049216910 0.047317795 0.448706474 -0.005560789 -0.13410384 -0.3816987680 -0.277767839 -0.246852220 0.07408401 0.03022269 0.222615075 0.02328394 -0.110521548 0.202986826 0.141392838 -0.26453802 0.12746162 -0.21289484 -0.038046246 -0.1030360136 0.07468120 0.017414752 0.240163493 -0.001822979 0.12683330 0.31389759 0.0614192179
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> ## until the updated GSVAdata goes through the build system
> ## remove duplicated rows
> fnames <- featureNames(huangArrayRMAnoBatchCommon_eset)
> mask <- duplicated(fnames)
> huangArrayRMAnoBatchCommon_eset <- huangArrayRMAnoBatchCommon_eset[!mask, ]
> pickrellCountsArgonneCQNcommon_eset <- pickrellCountsArgonneCQNcommon_eset[!mask, ]
>
> 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)
> 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)
> 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)
> 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 Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu
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>
> ## 2024-10-25 regression test script for method ssGSEA
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2024-10-25)
> 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 1.1025783 -0.9348073 1.2604604 -0.5213579 -0.1449497
g2 1.1178965 -1.1697762 -0.6188039 -1.5167080 -1.1104456
g3 -1.8181019 -1.1516529 0.9891236 -1.0173901 0.7009874
g4 -0.1944140 -0.3479166 -0.7471371 -0.6796938 1.5027270
g5 -0.6131956 1.0524922 -0.5313147 0.6119898 0.3619898
> 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 -0.10710844 -0.0075402860 0.018111634 0.06826270 0.26014254 0.17594978 0.087973512 0.055819757 0.15700598 0.269121740 0.14268720 0.04086184 0.242792242 -0.116646817 0.273503264 0.22672951 0.15528395 -6.274306e-03 0.08929691 0.0937292053 -0.18826347 -0.032007418 0.24725506 0.16250202 0.40627671 -0.011970337 0.116525140 0.188007670 -0.15080364 0.186273131
gs2 0.14876332 0.0540144335 0.021059857 0.12227647 0.19983120 0.06554688 0.116804681 0.155505534 0.15743888 0.270202424 0.09181943 0.11095440 0.064872954 0.089543470 0.135232572 0.10214918 0.07915424 5.605620e-02 0.25843907 0.1059282588 0.10528263 0.045431345 0.03787388 0.06283538 0.06531166 0.003237949 0.121625434 0.079708324 0.10991718 0.057063381
gs3 0.16158581 0.0362147810 0.239959504 0.09642318 0.05198813 0.19270533 0.253436184 0.150208238 0.15181052 0.055576713 0.15669853 0.10899963 -0.026981653 0.115084550 0.149710481 0.14955783 0.10199473 2.447883e-01 0.17069083 0.0804707944 0.02923656 0.150408363 0.11077462 0.04675553 0.03562779 -0.001602987 0.192244766 0.059315692 0.08455190 0.123420372
gs4 0.14589564 0.0864683263 -0.010929054 -0.16113206 -0.02369876 0.34222389 0.177908272 0.102132126 0.32529702 0.151161314 0.02429086 -0.16198474 0.191879194 0.088235520 0.004571591 0.36625561 0.22671433 6.435025e-02 0.31673822 -0.0172415327 0.13927111 0.060853788 0.16255204 0.04510571 -0.13286636 0.147530964 0.136776481 0.006949498 0.20814247 0.217102735
gs5 0.16477593 0.1375497879 0.200668301 0.21112512 0.09852523 0.17583094 0.030826930 0.201606752 0.18918451 0.114024960 0.16922362 0.16034306 0.048557592 0.071690328 0.125322906 0.05962545 0.09740882 3.785452e-02 0.11383181 0.1826365769 0.26317714 0.114697028 0.22904839 0.12690059 0.04997630 0.104694828 0.181219723 0.066936100 -0.05559892 0.144715578
gs6 0.21930119 0.2277281543 0.101798042 0.11786328 0.21268772 0.10177389 -0.087627083 0.217410745 0.09920588 0.020516900 0.20660549 0.15407158 0.033584165 0.045221846 0.060363175 0.09138202 0.11404948 5.369733e-02 0.15651701 0.1750682757 0.17807747 0.024454124 0.04306554 0.16177816 0.17400483 0.095143946 0.018599110 0.102109516 0.20845133 0.013869891
gs7 0.08886744 0.0239964398 0.154613405 0.01222809 0.10250532 0.15487584 0.175222062 0.007635356 0.20759893 0.026275511 0.09881399 -0.01351474 0.019442866 -0.075314324 0.105222267 0.03537408 0.04265941 9.041633e-03 0.16157915 0.0556808485 0.08688865 0.157798708 -0.04152628 0.14054050 0.15938786 0.165414775 0.113332471 0.123548589 0.04758883 0.221622133
gs8 0.10476715 0.1926843328 0.086990828 0.08528314 0.04744406 0.14473083 0.090295747 0.224587404 0.17659791 0.126743379 0.16659601 0.03167230 0.127524690 0.198639479 -0.018237682 0.04603435 0.14209656 1.315741e-01 0.17355687 0.1148370896 0.22166815 0.196094569 0.16894003 0.01132838 0.06453136 0.093140427 0.131495713 0.160444771 0.17191665 0.082907753
gs9 0.02170577 -0.0035409557 0.138671030 0.08120282 0.09175444 0.01359495 0.174364593 -0.066571474 0.21031287 0.013303152 0.18321591 0.04716510 0.240066285 -0.006297984 0.121995560 0.05794932 0.12727781 3.726694e-03 0.19940995 0.1609497811 0.13925776 0.051080383 0.18487588 0.15732052 0.06611793 0.135537204 0.257931518 0.196803611 0.22734507 0.406655547
gs10 -0.23836578 0.3319984306 0.287159051 -0.02356637 0.26670629 -0.11508821 0.255951952 0.085145273 -0.11993450 0.218441188 -0.03758299 0.11251991 -0.230176050 -0.134292490 0.258929873 0.10543338 -0.21325697 2.491196e-01 -0.07405134 0.1374205200 0.19875679 0.256439699 -0.13033622 0.23849232 0.22290960 0.308429465 0.100857487 0.311391866 0.16373044 0.129273255
gs11 0.16565095 0.2406594642 0.034999318 0.13008391 0.13988431 0.22211368 -0.007251999 0.049514438 0.16261333 0.179352717 0.06405095 0.05498569 0.106402881 0.028084660 0.225217392 0.12752824 0.16429576 1.754437e-01 0.18417741 0.0760651921 0.13877659 0.126906774 0.09934686 0.10896815 0.18656617 -0.011573427 0.102457568 0.160669510 0.15139884 0.206872269
gs12 0.03663285 0.1030081926 -0.001015873 0.03139407 0.10317782 0.15813694 0.100710587 0.069407197 0.09765120 0.068014936 0.02673928 0.08253175 0.043511859 0.145691788 0.045788167 0.11589384 0.15855849 5.808049e-02 0.07285050 0.1129467308 0.11275348 0.073963749 0.05298509 0.08670877 0.13269002 0.094275209 0.156012042 0.098769630 0.17797682 0.153172221
gs13 0.14478232 -0.0603905877 0.061063549 0.08377235 -0.04707064 0.03163759 0.238935417 0.119479749 0.21375144 0.026427433 0.05018396 0.04860360 0.173170557 0.172306657 0.068476181 -0.01296238 0.17033755 1.747676e-01 0.08866445 0.0906104912 -0.06289114 0.216497122 0.20370714 -0.10890679 -0.12468237 0.049231700 0.141729491 0.190747295 0.12011290 0.064787183
gs14 -0.11894533 0.0419944529 0.220356145 0.11646632 0.01716919 0.14490328 0.156901109 0.160689331 -0.05329918 0.038931352 0.16661327 0.01084037 -0.121101548 0.065153051 -0.027050960 0.18468218 0.05912851 1.103971e-01 0.06784390 0.0891054222 0.23249364 0.011123408 0.11876109 0.12637323 0.04506190 0.144826108 0.135083820 0.045376034 0.13147126 0.191934255
gs15 0.03840160 0.0761129062 0.105246115 0.13798361 0.04824562 0.20124839 0.107488556 0.105358806 0.13221891 0.084816081 0.19278169 0.16570474 0.057733791 0.092569500 0.169698483 0.13986877 0.02570140 1.203015e-01 0.18595957 0.0114428963 0.05252686 0.106218105 0.14053456 0.20637859 0.07774724 0.085428355 0.047515616 0.055603440 0.11689153 0.120794876
gs16 0.01910301 0.0835466268 0.033205254 0.06455267 0.08435620 0.04324494 0.073916860 0.161618450 0.09491475 0.154501578 0.11704125 0.04899138 0.105990696 0.040910519 0.002240644 0.09010372 0.04726274 -4.814234e-02 0.03227425 -0.0467711178 0.09406560 -0.006555519 0.12905385 0.02466134 0.06132676 0.147254694 0.132122950 0.186209290 0.21460582 0.172850600
gs17 0.13531212 0.0727876151 0.161692703 0.21252373 0.10996062 0.11293648 0.199935587 0.031682071 0.06801955 0.053595697 0.14104554 0.11005561 0.137837117 0.177522832 0.112475868 0.01588810 0.11285294 -6.438446e-02 0.07045567 0.1918428806 0.23462823 0.165998219 0.12189822 0.23358755 0.19092003 0.065357560 0.132155795 0.125468161 0.04760345 0.071750466
gs18 0.11164363 0.1457517538 0.071880269 0.13140946 0.12723124 0.13854399 0.099727823 0.146749400 0.05046031 0.133589555 0.13455580 0.05810720 0.003976583 0.164008622 0.115327842 0.05277884 0.03718150 2.360514e-01 0.15718982 0.1621912089 0.18244684 0.116627442 0.12374984 0.03311261 0.07095647 0.057452335 0.165345967 0.188366534 0.05621551 0.037010050
gs19 0.17148928 0.0001568614 0.161354396 0.03963361 0.01722683 0.27053958 0.027246051 0.160821098 0.35916273 0.075353860 -0.35848862 0.20235825 0.214669007 0.031603879 0.010752476 0.11407582 0.12424563 3.671759e-01 0.26364703 -0.1646490384 0.04748660 0.220019022 0.23824032 0.18495081 0.28209706 0.172556585 0.262395175 -0.058239752 -0.10625814 -0.035915588
gs20 0.03407852 0.1286337783 0.062235086 0.02626321 0.11770363 0.08253762 -0.003595976 0.176301723 0.18382297 0.194084606 0.23330511 0.09719188 0.250782880 0.123325999 0.102642028 0.18936429 0.33252153 6.661523e-05 -0.02233745 0.0822518036 0.28279492 0.151217097 0.12609872 0.26125967 0.09265097 -0.091603439 0.209704160 0.149067892 -0.07612640 0.165025321
gs21 0.09442664 0.0878367155 0.083321285 0.11129435 0.07487749 0.06783110 0.071169082 0.146490322 0.09099648 0.006027854 0.08492186 0.10071572 0.182375533 0.173030339 0.109743451 0.06105662 0.18287972 9.816697e-02 0.16142871 -0.0004335035 0.08635469 0.058130432 0.03283150 0.12574751 0.15019911 0.116818493 0.043379076 0.038116692 0.10674235 0.024699748
gs22 0.29616870 -0.0165339290 0.244278009 0.22897506 0.21569259 0.03316285 0.056597493 0.112946960 0.17390783 0.149635466 0.24181445 0.16663896 0.046362496 0.218778672 0.024596163 0.11783857 -0.06169079 -1.096825e-01 0.16481952 0.0927122691 -0.22839865 -0.024067835 -0.16321536 0.22928259 0.19958901 0.266208430 0.268555571 -0.075234997 0.14478010 0.272274378
gs23 0.16205651 0.1085841715 0.004174150 -0.01853907 -0.07551221 0.19257883 0.132782360 0.040119908 0.16067202 0.224055777 0.06617441 0.01757249 0.101610802 0.044258840 0.074248633 0.16549588 0.05575276 6.711687e-02 0.17634069 0.1523920529 0.18259277 0.006300758 0.08443370 0.22843575 0.15289306 0.157543521 0.004453404 0.228309501 0.04986206 0.114089181
gs24 0.12744638 0.1171658880 0.087451599 0.19238034 0.24821501 0.24776090 0.156747128 0.202793379 0.09849415 0.069002634 0.08661215 0.03641551 0.167816443 0.087480458 0.128927465 0.15500111 0.13074890 1.429781e-01 0.18422435 0.1329192877 0.12632530 0.127040505 0.02123643 -0.03121284 0.15966082 0.150162127 0.152485817 0.128568429 0.27875444 -0.008848817
gs25 0.10870481 0.0300737358 0.167118322 0.13554109 0.12564946 0.12908779 0.125872025 0.138903092 0.07769753 0.151376143 0.13412026 0.06301572 0.016512014 0.143046925 0.060385229 0.09403300 0.09011466 1.000454e-01 0.06157109 0.0991045239 0.12279758 0.253940846 0.13568681 0.09514299 0.10352198 0.068370673 0.128229857 0.072290480 0.20559555 0.070210776
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> ## until the updated GSVAdata goes through the build system
> ## remove duplicated rows
> fnames <- featureNames(huangArrayRMAnoBatchCommon_eset)
> mask <- duplicated(fnames)
> huangArrayRMAnoBatchCommon_eset <- huangArrayRMAnoBatchCommon_eset[!mask, ]
> pickrellCountsArgonneCQNcommon_eset <- pickrellCountsArgonneCQNcommon_eset[!mask, ]
>
> 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)
> 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 0.21721983 0.18996785 0.20541802 0.21636999 0.228918711 0.20965435 0.22509442 0.2235649655 0.220977222 0.21472697 0.21916441 0.220872497 0.20929258 0.21025902 0.20503366 0.20002652 0.19737894 0.1915313816 0.225171727 0.21722501 0.20442539 0.201715078 0.19389845 0.23136672 0.2215222396 0.212502607 0.22812038 0.221224253 0.204353401 0.2189767209 0.222743312 0.229498351 0.22080396 0.20317828 0.21913890 0.215767375
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.32446168 0.33049406 0.31884595 0.30778040 0.322825961 0.31549239 0.31984749 0.3186253154 0.329884236 0.31286516 0.32686043 0.331932334 0.31520004 0.32292166 0.31033759 0.31226198 0.30735116 0.3169153941 0.320574586 0.32927871 0.31034821 0.313491489 0.32322380 0.32454467 0.3077295170 0.302026455 0.31443410 0.325026294 0.324331257 0.3207569835 0.313222653 0.322386067 0.32321091 0.31485179 0.32985610 0.323056595
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.32631340 0.29204422 0.32185699 0.31933707 0.327513824 0.32317246 0.31703064 0.3269409336 0.317967058 0.30574471 0.32082637 0.325425815 0.31570330 0.32224347 0.30440257 0.31213747 0.30065861 0.3175689706 0.313330007 0.31543774 0.31510779 0.312095463 0.31153241 0.31362242 0.3132282287 0.305566472 0.31325712 0.318608621 0.309384440 0.3169379532 0.307955239 0.319524108 0.30335555 0.31482507 0.31942853 0.327111509
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.14182627 0.15211647 0.14271965 0.07976681 0.105400252 0.13016198 0.11308442 0.1603923704 0.141745067 0.09916369 0.16442237 0.158782258 0.10833470 0.17684148 0.13426092 0.11420977 0.14198863 0.1430677974 0.147053335 0.14852317 0.17190386 0.138824792 0.12229741 0.11695718 0.1094203746 0.069661903 0.14073541 0.182091703 0.114802588 0.1892910845 0.130613078 0.111700323 0.14423809 0.12352402 0.12239871 0.138517034
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.15589670 0.11795124 0.14733246 0.18726742 0.200179743 0.16460420 0.16814668 0.1803802820 0.170651270 0.18705111 0.18269329 0.164689570 0.16802619 0.17156053 0.16624099 0.14549160 0.13417407 0.1380493809 0.169178867 0.19245515 0.19070812 0.157703935 0.12731027 0.18645181 0.1952875908 0.176668101 0.19832418 0.161645680 0.152215693 0.1738055901 0.187529032 0.197625166 0.17265418 0.16157298 0.17927827 0.180461216
KEGG_GALACTOSE_METABOLISM 0.11185015 0.10303851 0.11114710 0.13762911 0.166229899 0.14462814 0.12737125 0.1372223140 0.143127853 0.15288235 0.15242597 0.150015563 0.15025630 0.14641113 0.12005469 0.11583190 0.11616116 0.1150820655 0.149767286 0.16914156 0.16521804 0.123969626 0.09231554 0.14960607 0.1765509593 0.129242228 0.17104478 0.137921945 0.112938564 0.1399801929 0.144929790 0.159188497 0.13460516 0.12474294 0.15643452 0.170268454
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.04264010 -0.03231123 0.01452384 -0.01036832 -0.021910717 -0.03141318 -0.01011631 0.0665210061 -0.006902107 -0.02868722 0.01181211 0.001943343 -0.01396127 0.03484297 -0.03185196 -0.01755440 -0.01490230 -0.0023964829 0.027566134 -0.04844573 -0.11519624 -0.008424876 -0.01168678 -0.02052165 0.0009019816 -0.002966386 -0.11321544 0.027588713 -0.020395271 0.0504415468 0.024212180 0.004538288 0.02797590 -0.01407919 -0.01892488 0.007548007
KEGG_FATTY_ACID_METABOLISM 0.19183128 0.17744988 0.19250355 0.18184509 0.195341708 0.17331431 0.18747206 0.2096229722 0.189591529 0.17790897 0.17750849 0.187869753 0.17494495 0.18089300 0.17590931 0.16301176 0.17738479 0.1849919449 0.187438993 0.17632413 0.15161479 0.184412247 0.17559254 0.18563812 0.1645376075 0.179295725 0.15698821 0.189770625 0.183474439 0.1897408272 0.186139806 0.195803395 0.20428606 0.18329585 0.17999004 0.186395203
KEGG_STEROID_BIOSYNTHESIS 0.29524811 0.29529433 0.26305985 0.27916683 0.291369504 0.28611129 0.30488156 0.3029092157 0.306255676 0.26810882 0.29474406 0.281947459 0.28373972 0.30315304 0.30913403 0.26600805 0.26954889 0.3018917086 0.272501281 0.28932257 0.27874550 0.272988159 0.28296743 0.28604081 0.2974946694 0.264534612 0.26805495 0.276212036 0.286420777 0.3080208857 0.289250451 0.299843542 0.29282928 0.29953128 0.29475944 0.287624480
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS -0.03527686 -0.09206897 -0.04724951 0.05922845 -0.123040372 -0.08440223 -0.02247123 -0.0444895464 -0.063808673 -0.15011601 -0.07680543 -0.027420724 -0.03119158 -0.08959075 -0.12837025 -0.15420608 -0.15144271 -0.0006081975 -0.141766799 -0.12405389 -0.14911801 -0.051949731 -0.06070369 -0.03605965 -0.1464126356 -0.128765886 -0.15301862 0.017645099 0.013456000 0.0212309112 -0.008194779 -0.079071591 -0.01500256 -0.09495015 -0.12155351 -0.100440547
KEGG_STEROID_HORMONE_BIOSYNTHESIS -0.00557581 -0.04856694 -0.07962122 -0.01634905 -0.091044018 -0.04599868 -0.05768200 -0.0074510201 -0.032139943 -0.04874069 0.01286925 -0.026577359 -0.05129199 -0.03421180 -0.09091778 -0.04584484 -0.06287348 -0.0034919294 -0.083543200 -0.04389054 -0.07381303 -0.041702930 -0.06695905 -0.06192588 -0.0227702629 -0.063490224 -0.05022174 -0.046592348 -0.007548499 -0.0308809908 0.039232151 -0.057971384 0.01429542 -0.04122957 -0.10027592 -0.022232617
KEGG_OXIDATIVE_PHOSPHORYLATION 0.23497936 0.26556806 0.26354533 0.24733681 0.255381506 0.25170841 0.25458089 0.2568403676 0.246695570 0.25779092 0.25802374 0.247747022 0.25323279 0.26055543 0.24846320 0.24628500 0.25194750 0.2622938525 0.253222517 0.24479145 0.24463543 0.248384064 0.24603574 0.26103437 0.2524703309 0.259547718 0.25726942 0.244747666 0.244996475 0.2471416259 0.249469042 0.253249454 0.25628033 0.26143053 0.26144384 0.249062840
KEGG_PURINE_METABOLISM 0.11325584 0.11332828 0.13077673 0.12893752 0.130817932 0.12561449 0.12720947 0.1256873440 0.114700735 0.11788264 0.12747490 0.124280253 0.12512453 0.12946903 0.11873267 0.11061891 0.11863947 0.1308693330 0.121043210 0.11896563 0.12491349 0.118883839 0.11022199 0.12366477 0.1117663302 0.125384977 0.12630639 0.120610144 0.116815136 0.1210626033 0.125983950 0.120815453 0.12099075 0.12316753 0.11800994 0.119580506
KEGG_PYRIMIDINE_METABOLISM 0.17800387 0.17527065 0.19884535 0.19701890 0.184777785 0.18903706 0.19454189 0.1915954305 0.176950850 0.18800446 0.18769787 0.191255069 0.17718099 0.19361466 0.18615347 0.18077753 0.18542345 0.1964488373 0.174531528 0.18933558 0.18810401 0.175298859 0.17764859 0.19064730 0.1772305033 0.198975792 0.18500821 0.173320601 0.179735366 0.1736996771 0.177995754 0.185681551 0.19296710 0.19237550 0.17700142 0.185011599
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.11018091 0.09294768 0.09093082 0.09992257 0.110831140 0.08971302 0.10840243 0.1024259643 0.098931566 0.09485157 0.10432982 0.113144923 0.09856275 0.09881155 0.10840186 0.10220347 0.09481083 0.0891737271 0.115000274 0.12387476 0.09915763 0.096112403 0.08818501 0.11116253 0.1016561395 0.090437660 0.10035184 0.114025237 0.088853019 0.1119400206 0.102128997 0.091755227 0.08657544 0.10471612 0.09690680 0.114057430
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.07628668 0.01307178 0.03101003 0.05515989 0.075463953 0.04673004 0.05698317 0.0723469694 0.092114623 0.05565018 0.08771003 0.050476883 0.05982430 0.06093465 0.08411111 0.10257639 0.01534408 0.0049506028 0.049345045 0.07073074 0.05144714 0.045243833 0.05156095 0.06443263 0.0854631978 0.053141309 0.06161289 0.050620090 0.064627852 0.0692397313 0.068054801 0.075245655 0.03343401 0.05209816 0.09375715 0.070300250
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.25918823 0.22908633 0.23931943 0.24468764 0.251224655 0.23650854 0.24676096 0.2544249892 0.257027419 0.24181180 0.26158127 0.245785017 0.24380308 0.24911075 0.26862100 0.25537591 0.22958776 0.2350093908 0.238041909 0.24118880 0.26569055 0.234649830 0.23413561 0.23312136 0.2583443901 0.215868622 0.23487909 0.256747679 0.240069729 0.2503534031 0.237280277 0.252814643 0.22675799 0.23882384 0.25746678 0.244663768
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.18883424 0.18650551 0.17557638 0.15658617 0.178655772 0.18085341 0.18591447 0.1965965285 0.191986472 0.14239247 0.20175131 0.181876584 0.18804991 0.18232923 0.18887323 0.17039133 0.16977864 0.1678429938 0.183820453 0.19763988 0.16368082 0.161257462 0.15806295 0.18377007 0.1711229256 0.163882200 0.15084200 0.197174191 0.185732185 0.1982308514 0.174408250 0.182924303 0.17837675 0.16090692 0.19907645 0.190470297
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.28597966 0.28257466 0.24987352 0.24513138 0.270809700 0.29659978 0.25835465 0.2522956908 0.282009158 0.24763585 0.32062187 0.275069920 0.28305890 0.30041147 0.30306313 0.29139854 0.28285654 0.2580612581 0.267239527 0.32469106 0.29207908 0.267323752 0.24763192 0.28306454 0.2938935043 0.262322661 0.29456652 0.269466310 0.263418681 0.2668145469 0.261212111 0.251367355 0.25148998 0.28433772 0.31307106 0.299593259
KEGG_LYSINE_DEGRADATION 0.11407442 0.09382349 0.11782931 0.11941889 0.114473142 0.11464425 0.11389916 0.1284496058 0.110734405 0.10309803 0.10924074 0.120264909 0.11123369 0.09948345 0.10405039 0.09181117 0.11042324 0.0994052703 0.114472046 0.11125822 0.10546333 0.095505038 0.09685105 0.10334061 0.1086062981 0.114488680 0.09122678 0.108374699 0.111399195 0.1171784351 0.104032100 0.110409819 0.10448105 0.09261547 0.10754065 0.112386623
KEGG_ARGININE_AND_PROLINE_METABOLISM 0.12764946 0.12055210 0.12816676 0.12793214 0.140381579 0.11267991 0.13893640 0.1364776104 0.118545890 0.12529668 0.13403358 0.119966520 0.12679147 0.11430758 0.12770117 0.12067034 0.11125538 0.1062000915 0.135324575 0.11397563 0.11288549 0.120517853 0.10901776 0.13682578 0.1483193221 0.127679567 0.12056048 0.130073940 0.120173269 0.1435536666 0.139448087 0.139822706 0.12657002 0.12322466 0.13683535 0.130249707
KEGG_HISTIDINE_METABOLISM 0.01094636 -0.00936846 -0.02466989 -0.03984077 -0.003726944 -0.02847858 -0.02499903 0.0008721746 -0.015007978 -0.03171141 -0.03673702 -0.017681608 -0.04403008 -0.03539251 -0.02405048 -0.02933671 -0.02621412 -0.0312195354 0.009365323 -0.04673035 -0.06843640 -0.022694260 -0.03062155 -0.03676474 -0.0255030415 -0.039825198 -0.08617490 0.004277051 -0.029682747 -0.0003703405 -0.019976169 -0.027051070 -0.01093124 -0.03008042 -0.02124978 -0.035520407
KEGG_TYROSINE_METABOLISM 0.06753397 0.05290119 0.05770778 0.04349213 0.057272553 0.05836395 0.05858804 0.0509600740 0.058842036 0.04745176 0.05780087 0.046945575 0.04964383 0.06579719 0.07188325 0.05398455 0.05778994 0.0691937578 0.044447478 0.04366717 0.06340185 0.067264165 0.04899601 0.05360736 0.0526043668 0.041290409 0.04403640 0.064516224 0.055322021 0.0484423707 0.070088304 0.042856073 0.06603251 0.06558193 0.05869159 0.057652972
KEGG_PHENYLALANINE_METABOLISM 0.11963716 0.09622739 0.09466570 0.09056768 0.091218014 0.09184515 0.09985165 0.0975407386 0.104921261 0.08747543 0.09590836 0.092070748 0.10457927 0.09912605 0.10427463 0.10698595 0.07948661 0.0989468131 0.119134895 0.09914608 0.10452572 0.086232868 0.09680196 0.10514388 0.0976260981 0.085916976 0.09975787 0.107143882 0.084064813 0.0915211900 0.102144015 0.107409575 0.10266364 0.09500716 0.08808469 0.098433629
KEGG_TRYPTOPHAN_METABOLISM 0.12740929 0.13577138 0.12025881 0.10215757 0.105727984 0.10296569 0.11271988 0.1473129592 0.134446344 0.09439503 0.12408323 0.114771330 0.10218883 0.12975022 0.09530952 0.11916134 0.10779215 0.1239415799 0.126037527 0.11886633 0.06676474 0.112630341 0.11228894 0.10030582 0.1180285091 0.113713721 0.09177254 0.132651298 0.110507418 0.1204234839 0.125432246 0.116328296 0.14711772 0.12007138 0.10448497 0.118966894
> pickrellPar <- ssgseaParam(pickrellCountsArgonneCQNcommon_eset,
+ canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
> 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 0.255973871 0.234244836 0.22340103 0.25147113 0.25604502 0.22418622 0.26808957 0.24342921 0.22291266 0.24434352 0.241461667 0.24764348 0.240706877 0.26427645 0.25153628 0.221695112 0.25933664 0.257579414 0.237132544 0.23355947 0.24083186 0.24377961 0.24398934 0.253362819 0.229899549 0.232863910 0.25288826 0.25070805 0.2350691397 0.25292904 0.25386372 0.23975752 0.23464696 0.24542300 0.25626878 0.25051771
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.276721079 0.263644751 0.24671314 0.27511916 0.27544540 0.24952920 0.28813898 0.26719607 0.22432070 0.25808503 0.264374411 0.26609297 0.267760618 0.27281530 0.26932935 0.218624667 0.28127101 0.273970441 0.253553333 0.25911760 0.26054107 0.26844807 0.27055856 0.265170337 0.243920672 0.241108955 0.28510006 0.28097655 0.2407076495 0.26191338 0.26220803 0.27378757 0.25408726 0.26875884 0.27358412 0.26446288
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.308020808 0.297901469 0.28989411 0.31299315 0.31062622 0.29557813 0.33138058 0.30891326 0.27198469 0.29291718 0.318217559 0.31734453 0.303133878 0.32976745 0.31585270 0.275896528 0.32122060 0.328762461 0.288492608 0.28968383 0.29747578 0.29393201 0.30385264 0.308813494 0.284093229 0.286685677 0.32273350 0.31658653 0.2937498126 0.30270973 0.30274210 0.30105302 0.29975257 0.30855189 0.29564512 0.31094443
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.072490776 0.057665424 0.05042026 0.05497896 0.06838128 0.07721215 0.08165341 0.09208236 0.03505170 0.09123428 0.097520413 0.06906502 0.081204820 0.14558660 0.10070838 0.031256469 0.09159758 0.115363944 0.088310700 0.08098270 0.11279059 0.04548519 0.05879566 0.091246266 0.044849846 0.014590393 0.11201919 0.13581918 0.0576718138 0.07863358 0.10737231 0.06168125 0.10049004 0.07836096 0.04773881 0.08027239
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.178853698 0.181117241 0.18127676 0.20618109 0.16474691 0.15651927 0.20496583 0.18186585 0.12796430 0.18919793 0.194352045 0.18648633 0.191330063 0.18583711 0.21655450 0.163603168 0.20121985 0.213403292 0.170896337 0.18299748 0.17715740 0.18020032 0.18630756 0.208329171 0.182319139 0.186208415 0.20214840 0.14286122 0.1689044226 0.17558507 0.20034137 0.16248263 0.16171966 0.19872350 0.18448376 0.20468815
KEGG_GALACTOSE_METABOLISM 0.180866571 0.159543878 0.16227291 0.20539900 0.18018335 0.15498483 0.21922691 0.17807913 0.12333373 0.18313170 0.198801246 0.19418260 0.190226610 0.19518870 0.22219754 0.149177439 0.20534732 0.200288866 0.169905819 0.18195222 0.18920139 0.17577461 0.16963025 0.194575390 0.198051080 0.192049056 0.22210179 0.15370205 0.1631961787 0.17220540 0.20561062 0.15856520 0.15381957 0.18863664 0.18887519 0.20809743
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.075839356 0.079870770 0.01839691 0.05295801 0.05594010 0.03619848 0.08085292 0.05211813 0.02046458 0.09556844 0.045945102 0.03536734 0.072302956 0.13924114 0.04048614 0.000868274 0.08528874 0.108627906 0.054713382 0.01778929 -0.08069455 0.01882544 0.06240893 0.065481911 0.023139332 0.006485666 0.03032984 0.10225397 -0.0037549053 0.05275949 0.07459863 0.08237901 0.05589809 0.04198289 0.06239312 0.07388409
KEGG_FATTY_ACID_METABOLISM 0.189545892 0.170487970 0.14107909 0.19152027 0.20036184 0.16180871 0.20687596 0.18054223 0.16653839 0.17649890 0.168908518 0.17875348 0.178533717 0.20967324 0.17159817 0.130611489 0.20904897 0.197016502 0.164712821 0.15795025 0.16354191 0.17822402 0.18280684 0.187852572 0.113071322 0.130261054 0.17735453 0.19431706 0.1593913401 0.18846504 0.18883700 0.18933507 0.15945060 0.16646827 0.17874163 0.19724564
KEGG_STEROID_BIOSYNTHESIS 0.224203013 0.183303179 0.10596218 0.15398123 0.20660401 0.19357323 0.19895056 0.19354072 0.13738963 0.13250921 0.166087855 0.15449865 0.201680501 0.18416480 0.20216814 0.138593021 0.16130884 0.187533552 0.127409131 0.17258652 0.17184479 0.17658992 0.20496232 0.178032960 0.221859949 0.187127542 0.17884508 0.15830785 0.1559615607 0.17949533 0.21176210 0.18619753 0.20543338 0.21969290 0.24219179 0.17351891
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 0.006756532 -0.045782593 -0.05681410 0.07110818 -0.03839128 -0.06537417 -0.01691239 -0.01174482 -0.07123455 -0.07226010 -0.041041770 -0.01482012 0.004425068 0.04992665 -0.04779878 -0.071089965 -0.04307171 -0.017284164 -0.035488641 -0.06358435 -0.04624196 -0.03151707 -0.02267855 -0.004022051 -0.083034638 -0.065514503 -0.04784385 -0.03744402 -0.0005655492 0.03696114 0.04582892 -0.02683713 -0.04880944 -0.05773766 -0.04101500 -0.03689178
KEGG_STEROID_HORMONE_BIOSYNTHESIS -0.046658311 -0.094049506 -0.13823804 -0.05907553 -0.11515098 -0.04435061 -0.07844386 -0.07347585 -0.10065156 -0.06042842 -0.052315196 -0.07130284 -0.082016425 -0.04890030 -0.08818966 -0.080981150 -0.09427154 -0.072991221 -0.132047304 -0.06463561 -0.13630508 -0.09083536 -0.11657925 -0.086356880 -0.095038994 -0.120331272 -0.07225945 -0.03510727 -0.0668165610 -0.10586318 0.02671161 -0.04934596 -0.05349457 -0.11643009 -0.12958753 -0.06607392
KEGG_OXIDATIVE_PHOSPHORYLATION 0.289875603 0.306180274 0.26008466 0.29541751 0.29439500 0.28659621 0.31500729 0.29204880 0.29611294 0.28171311 0.288757552 0.29818332 0.295881714 0.30697427 0.29386532 0.297765229 0.29571081 0.303990507 0.280545983 0.28709475 0.29820052 0.30086013 0.29124721 0.294101932 0.251997289 0.264215516 0.29632865 0.30623682 0.3065889480 0.28923030 0.30193543 0.30177690 0.31174532 0.28598468 0.28879303 0.28703293
KEGG_PURINE_METABOLISM 0.121199616 0.113729580 0.11003028 0.13065417 0.11798635 0.10826198 0.12913892 0.12009178 0.08407076 0.11195380 0.112481215 0.11494730 0.105008038 0.13116526 0.11960315 0.112557873 0.12856140 0.122682619 0.119374712 0.10548339 0.10871674 0.11069066 0.10468173 0.108918495 0.098684948 0.102537595 0.12680997 0.13711068 0.1139065356 0.12013213 0.10935277 0.11335705 0.10240861 0.11724310 0.10688270 0.11146964
KEGG_PYRIMIDINE_METABOLISM 0.159364219 0.145034413 0.14683938 0.17367689 0.15303132 0.14746795 0.16815099 0.15853649 0.11338321 0.15119996 0.146658541 0.15150584 0.126621736 0.17142933 0.15824172 0.142391725 0.16265716 0.161071263 0.147383996 0.14114834 0.14627424 0.14142842 0.14494780 0.146013445 0.114023679 0.130659164 0.16539603 0.18053868 0.1511483017 0.16018537 0.13583283 0.16226122 0.13939515 0.15512501 0.13584431 0.15347271
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.112508883 0.074202209 0.08660117 0.09207883 0.11280671 0.09472827 0.09704054 0.07733135 0.10943575 0.07564145 0.076565645 0.07899580 0.081264824 0.10757013 0.09734334 0.046542835 0.08917489 0.076487510 0.091295210 0.07796498 0.07171296 0.08706823 0.06550663 0.087144765 0.072742315 0.070136832 0.10741914 0.09203473 0.0631336245 0.12192789 0.08543094 0.06735452 0.05914758 0.07996024 0.08585010 0.09660417
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.063066152 0.008244582 0.05888892 0.06656162 0.06755857 0.04379612 0.03310672 0.04702300 0.07188416 0.04974758 0.019198599 0.05230415 0.007011605 0.07932181 0.04631052 0.006101109 0.03600723 0.007179737 0.059641322 0.01372905 -0.02144312 0.04741604 0.03671989 0.033030921 0.058596958 0.025885885 0.05314484 -0.01905521 0.0344527035 0.09811477 0.03587761 0.02208787 -0.01476052 0.03810409 0.09572419 0.07020138
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.233841890 0.189564988 0.20507257 0.22829497 0.22708184 0.19891652 0.19829674 0.22080930 0.21841648 0.21549322 0.192090772 0.19635785 0.202624437 0.24415962 0.22573236 0.162311561 0.19762888 0.190417790 0.196717053 0.18142032 0.20830986 0.21357824 0.20096179 0.201421602 0.211807543 0.203022494 0.19715210 0.19397219 0.1831123581 0.22839547 0.18688488 0.20420093 0.17810573 0.19787799 0.21869417 0.22013221
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.149451223 0.130390435 0.11090077 0.15171054 0.15674850 0.12207153 0.17676341 0.13240117 0.14595322 0.12775620 0.154294491 0.13844160 0.147993017 0.18547995 0.14445481 0.099906770 0.16080600 0.158214170 0.127978549 0.13338533 0.12794009 0.13430359 0.13380999 0.163421828 0.097145942 0.107391342 0.15045297 0.15959356 0.1167283443 0.15777718 0.14485771 0.14543148 0.13887590 0.12885753 0.15223409 0.15723079
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.295049854 0.261601594 0.20403465 0.28738325 0.29603089 0.27196679 0.27622279 0.24595352 0.27911628 0.21938983 0.291009359 0.26240936 0.257169673 0.29805967 0.28918494 0.233479253 0.27807435 0.255999607 0.243017519 0.27438415 0.27711754 0.24764661 0.23187567 0.282690377 0.269031146 0.250755848 0.30790395 0.28484647 0.2548749648 0.27333689 0.26646895 0.24028977 0.27659068 0.24372431 0.28254069 0.28445791
KEGG_LYSINE_DEGRADATION 0.141445452 0.125002226 0.13255242 0.14247800 0.13445308 0.12163080 0.14683973 0.13350430 0.09455978 0.12203523 0.121846397 0.12672657 0.124437291 0.13792739 0.13711666 0.119280133 0.14191460 0.133529312 0.143966681 0.11140711 0.10524696 0.13044997 0.13773078 0.134887830 0.112264818 0.122763552 0.12934023 0.13530622 0.1228715577 0.13550145 0.12430132 0.13593479 0.10488655 0.13490541 0.13528939 0.14122687
KEGG_ARGININE_AND_PROLINE_METABOLISM 0.135482923 0.122800947 0.10546760 0.12529070 0.14881835 0.11780892 0.13985852 0.12241508 0.09404450 0.11735467 0.139880299 0.10924993 0.124094947 0.13132972 0.12119785 0.089756673 0.12963747 0.126783881 0.117471694 0.11395978 0.11733101 0.13675663 0.11316903 0.130174672 0.104091634 0.117336202 0.12537136 0.11143364 0.1056317091 0.14603708 0.13290068 0.10604271 0.10926022 0.12441688 0.14465486 0.12962314
KEGG_HISTIDINE_METABOLISM -0.031406167 -0.027028114 -0.05320652 -0.03884676 -0.03768201 -0.05311762 -0.03059749 -0.04403581 -0.04575910 -0.02307710 -0.069587330 -0.05100703 -0.063814721 -0.02769063 -0.05394060 -0.064034876 -0.03240874 -0.040189433 -0.028223850 -0.04656494 -0.06820722 -0.03735737 -0.02600696 -0.040982550 -0.045504413 -0.058399118 -0.06855384 -0.02182960 -0.0482012289 -0.03138879 -0.03374364 -0.03833469 -0.04428041 -0.03169806 -0.01319006 -0.03962329
KEGG_TYROSINE_METABOLISM 0.017084992 0.013181478 0.01268639 0.04713214 0.01176082 0.02979957 0.04417175 0.03403665 0.01332206 0.03659289 0.022255722 0.02675872 0.009888131 0.04903079 0.03012079 0.023843052 0.04643905 0.039686340 0.009885306 0.02695262 0.03836951 0.04709984 0.02558438 0.038489611 -0.012243132 0.006588370 0.04123095 0.02120107 0.0534860072 0.02777202 0.04696405 0.02599549 0.05481278 0.01839159 0.06080289 0.03592215
KEGG_PHENYLALANINE_METABOLISM 0.039223065 0.029140116 0.02737110 0.04131291 0.02543846 0.04082318 0.02604365 0.04681683 0.04448473 0.02668485 0.009443264 0.01801024 0.029907958 0.06543161 0.04981445 0.029020563 0.03200465 0.037690432 0.045323751 0.01243177 0.07294275 0.05536484 0.05322965 0.038324553 0.006928568 0.043245725 0.05273879 0.02880029 0.0305594156 0.04343878 0.06363048 0.02883049 0.02467284 0.04462306 0.06299359 0.01967917
KEGG_TRYPTOPHAN_METABOLISM 0.123047327 0.122664093 0.07570663 0.11492944 0.10828508 0.10297933 0.12667410 0.12674000 0.09130083 0.10170316 0.117485972 0.11432743 0.106990443 0.13120525 0.10417994 0.095119597 0.11195818 0.118766135 0.109696728 0.09143247 0.07791307 0.11149700 0.12123200 0.101461411 0.088796360 0.080136676 0.11191365 0.15854422 0.0951832300 0.11281184 0.12597991 0.13622521 0.12241147 0.10750563 0.12420200 0.11243731
>
> 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)
> 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
33.346 1.098 34.431
GSVA.Rcheck/tests/test_ssgsea_newapi.Rout.save
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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>
> ## 2024-10-25 regression test script for method ssGSEA
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2024-10-25)
> 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 1.1025783 -0.9348073 1.2604604 -0.5213579 -0.1449497
g2 1.1178965 -1.1697762 -0.6188039 -1.5167080 -1.1104456
g3 -1.8181019 -1.1516529 0.9891236 -1.0173901 0.7009874
g4 -0.1944140 -0.3479166 -0.7471371 -0.6796938 1.5027270
g5 -0.6131956 1.0524922 -0.5313147 0.6119898 0.3619898
> 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 -0.10710844 -0.0075402860 0.018111634 0.06826270 0.26014254 0.17594978 0.087973512 0.055819757 0.15700598 0.269121740 0.14268720 0.04086184 0.242792242 -0.116646817 0.273503264 0.22672951 0.15528395 -6.274306e-03 0.08929691 0.0937292053 -0.18826347 -0.032007418 0.24725506 0.16250202 0.40627671 -0.011970337 0.116525140 0.188007670 -0.15080364 0.186273131
gs2 0.14876332 0.0540144335 0.021059857 0.12227647 0.19983120 0.06554688 0.116804681 0.155505534 0.15743888 0.270202424 0.09181943 0.11095440 0.064872954 0.089543470 0.135232572 0.10214918 0.07915424 5.605620e-02 0.25843907 0.1059282588 0.10528263 0.045431345 0.03787388 0.06283538 0.06531166 0.003237949 0.121625434 0.079708324 0.10991718 0.057063381
gs3 0.16158581 0.0362147810 0.239959504 0.09642318 0.05198813 0.19270533 0.253436184 0.150208238 0.15181052 0.055576713 0.15669853 0.10899963 -0.026981653 0.115084550 0.149710481 0.14955783 0.10199473 2.447883e-01 0.17069083 0.0804707944 0.02923656 0.150408363 0.11077462 0.04675553 0.03562779 -0.001602987 0.192244766 0.059315692 0.08455190 0.123420372
gs4 0.14589564 0.0864683263 -0.010929054 -0.16113206 -0.02369876 0.34222389 0.177908272 0.102132126 0.32529702 0.151161314 0.02429086 -0.16198474 0.191879194 0.088235520 0.004571591 0.36625561 0.22671433 6.435025e-02 0.31673822 -0.0172415327 0.13927111 0.060853788 0.16255204 0.04510571 -0.13286636 0.147530964 0.136776481 0.006949498 0.20814247 0.217102735
gs5 0.16477593 0.1375497879 0.200668301 0.21112512 0.09852523 0.17583094 0.030826930 0.201606752 0.18918451 0.114024960 0.16922362 0.16034306 0.048557592 0.071690328 0.125322906 0.05962545 0.09740882 3.785452e-02 0.11383181 0.1826365769 0.26317714 0.114697028 0.22904839 0.12690059 0.04997630 0.104694828 0.181219723 0.066936100 -0.05559892 0.144715578
gs6 0.21930119 0.2277281543 0.101798042 0.11786328 0.21268772 0.10177389 -0.087627083 0.217410745 0.09920588 0.020516900 0.20660549 0.15407158 0.033584165 0.045221846 0.060363175 0.09138202 0.11404948 5.369733e-02 0.15651701 0.1750682757 0.17807747 0.024454124 0.04306554 0.16177816 0.17400483 0.095143946 0.018599110 0.102109516 0.20845133 0.013869891
gs7 0.08886744 0.0239964398 0.154613405 0.01222809 0.10250532 0.15487584 0.175222062 0.007635356 0.20759893 0.026275511 0.09881399 -0.01351474 0.019442866 -0.075314324 0.105222267 0.03537408 0.04265941 9.041633e-03 0.16157915 0.0556808485 0.08688865 0.157798708 -0.04152628 0.14054050 0.15938786 0.165414775 0.113332471 0.123548589 0.04758883 0.221622133
gs8 0.10476715 0.1926843328 0.086990828 0.08528314 0.04744406 0.14473083 0.090295747 0.224587404 0.17659791 0.126743379 0.16659601 0.03167230 0.127524690 0.198639479 -0.018237682 0.04603435 0.14209656 1.315741e-01 0.17355687 0.1148370896 0.22166815 0.196094569 0.16894003 0.01132838 0.06453136 0.093140427 0.131495713 0.160444771 0.17191665 0.082907753
gs9 0.02170577 -0.0035409557 0.138671030 0.08120282 0.09175444 0.01359495 0.174364593 -0.066571474 0.21031287 0.013303152 0.18321591 0.04716510 0.240066285 -0.006297984 0.121995560 0.05794932 0.12727781 3.726694e-03 0.19940995 0.1609497811 0.13925776 0.051080383 0.18487588 0.15732052 0.06611793 0.135537204 0.257931518 0.196803611 0.22734507 0.406655547
gs10 -0.23836578 0.3319984306 0.287159051 -0.02356637 0.26670629 -0.11508821 0.255951952 0.085145273 -0.11993450 0.218441188 -0.03758299 0.11251991 -0.230176050 -0.134292490 0.258929873 0.10543338 -0.21325697 2.491196e-01 -0.07405134 0.1374205200 0.19875679 0.256439699 -0.13033622 0.23849232 0.22290960 0.308429465 0.100857487 0.311391866 0.16373044 0.129273255
gs11 0.16565095 0.2406594642 0.034999318 0.13008391 0.13988431 0.22211368 -0.007251999 0.049514438 0.16261333 0.179352717 0.06405095 0.05498569 0.106402881 0.028084660 0.225217392 0.12752824 0.16429576 1.754437e-01 0.18417741 0.0760651921 0.13877659 0.126906774 0.09934686 0.10896815 0.18656617 -0.011573427 0.102457568 0.160669510 0.15139884 0.206872269
gs12 0.03663285 0.1030081926 -0.001015873 0.03139407 0.10317782 0.15813694 0.100710587 0.069407197 0.09765120 0.068014936 0.02673928 0.08253175 0.043511859 0.145691788 0.045788167 0.11589384 0.15855849 5.808049e-02 0.07285050 0.1129467308 0.11275348 0.073963749 0.05298509 0.08670877 0.13269002 0.094275209 0.156012042 0.098769630 0.17797682 0.153172221
gs13 0.14478232 -0.0603905877 0.061063549 0.08377235 -0.04707064 0.03163759 0.238935417 0.119479749 0.21375144 0.026427433 0.05018396 0.04860360 0.173170557 0.172306657 0.068476181 -0.01296238 0.17033755 1.747676e-01 0.08866445 0.0906104912 -0.06289114 0.216497122 0.20370714 -0.10890679 -0.12468237 0.049231700 0.141729491 0.190747295 0.12011290 0.064787183
gs14 -0.11894533 0.0419944529 0.220356145 0.11646632 0.01716919 0.14490328 0.156901109 0.160689331 -0.05329918 0.038931352 0.16661327 0.01084037 -0.121101548 0.065153051 -0.027050960 0.18468218 0.05912851 1.103971e-01 0.06784390 0.0891054222 0.23249364 0.011123408 0.11876109 0.12637323 0.04506190 0.144826108 0.135083820 0.045376034 0.13147126 0.191934255
gs15 0.03840160 0.0761129062 0.105246115 0.13798361 0.04824562 0.20124839 0.107488556 0.105358806 0.13221891 0.084816081 0.19278169 0.16570474 0.057733791 0.092569500 0.169698483 0.13986877 0.02570140 1.203015e-01 0.18595957 0.0114428963 0.05252686 0.106218105 0.14053456 0.20637859 0.07774724 0.085428355 0.047515616 0.055603440 0.11689153 0.120794876
gs16 0.01910301 0.0835466268 0.033205254 0.06455267 0.08435620 0.04324494 0.073916860 0.161618450 0.09491475 0.154501578 0.11704125 0.04899138 0.105990696 0.040910519 0.002240644 0.09010372 0.04726274 -4.814234e-02 0.03227425 -0.0467711178 0.09406560 -0.006555519 0.12905385 0.02466134 0.06132676 0.147254694 0.132122950 0.186209290 0.21460582 0.172850600
gs17 0.13531212 0.0727876151 0.161692703 0.21252373 0.10996062 0.11293648 0.199935587 0.031682071 0.06801955 0.053595697 0.14104554 0.11005561 0.137837117 0.177522832 0.112475868 0.01588810 0.11285294 -6.438446e-02 0.07045567 0.1918428806 0.23462823 0.165998219 0.12189822 0.23358755 0.19092003 0.065357560 0.132155795 0.125468161 0.04760345 0.071750466
gs18 0.11164363 0.1457517538 0.071880269 0.13140946 0.12723124 0.13854399 0.099727823 0.146749400 0.05046031 0.133589555 0.13455580 0.05810720 0.003976583 0.164008622 0.115327842 0.05277884 0.03718150 2.360514e-01 0.15718982 0.1621912089 0.18244684 0.116627442 0.12374984 0.03311261 0.07095647 0.057452335 0.165345967 0.188366534 0.05621551 0.037010050
gs19 0.17148928 0.0001568614 0.161354396 0.03963361 0.01722683 0.27053958 0.027246051 0.160821098 0.35916273 0.075353860 -0.35848862 0.20235825 0.214669007 0.031603879 0.010752476 0.11407582 0.12424563 3.671759e-01 0.26364703 -0.1646490384 0.04748660 0.220019022 0.23824032 0.18495081 0.28209706 0.172556585 0.262395175 -0.058239752 -0.10625814 -0.035915588
gs20 0.03407852 0.1286337783 0.062235086 0.02626321 0.11770363 0.08253762 -0.003595976 0.176301723 0.18382297 0.194084606 0.23330511 0.09719188 0.250782880 0.123325999 0.102642028 0.18936429 0.33252153 6.661523e-05 -0.02233745 0.0822518036 0.28279492 0.151217097 0.12609872 0.26125967 0.09265097 -0.091603439 0.209704160 0.149067892 -0.07612640 0.165025321
gs21 0.09442664 0.0878367155 0.083321285 0.11129435 0.07487749 0.06783110 0.071169082 0.146490322 0.09099648 0.006027854 0.08492186 0.10071572 0.182375533 0.173030339 0.109743451 0.06105662 0.18287972 9.816697e-02 0.16142871 -0.0004335035 0.08635469 0.058130432 0.03283150 0.12574751 0.15019911 0.116818493 0.043379076 0.038116692 0.10674235 0.024699748
gs22 0.29616870 -0.0165339290 0.244278009 0.22897506 0.21569259 0.03316285 0.056597493 0.112946960 0.17390783 0.149635466 0.24181445 0.16663896 0.046362496 0.218778672 0.024596163 0.11783857 -0.06169079 -1.096825e-01 0.16481952 0.0927122691 -0.22839865 -0.024067835 -0.16321536 0.22928259 0.19958901 0.266208430 0.268555571 -0.075234997 0.14478010 0.272274378
gs23 0.16205651 0.1085841715 0.004174150 -0.01853907 -0.07551221 0.19257883 0.132782360 0.040119908 0.16067202 0.224055777 0.06617441 0.01757249 0.101610802 0.044258840 0.074248633 0.16549588 0.05575276 6.711687e-02 0.17634069 0.1523920529 0.18259277 0.006300758 0.08443370 0.22843575 0.15289306 0.157543521 0.004453404 0.228309501 0.04986206 0.114089181
gs24 0.12744638 0.1171658880 0.087451599 0.19238034 0.24821501 0.24776090 0.156747128 0.202793379 0.09849415 0.069002634 0.08661215 0.03641551 0.167816443 0.087480458 0.128927465 0.15500111 0.13074890 1.429781e-01 0.18422435 0.1329192877 0.12632530 0.127040505 0.02123643 -0.03121284 0.15966082 0.150162127 0.152485817 0.128568429 0.27875444 -0.008848817
gs25 0.10870481 0.0300737358 0.167118322 0.13554109 0.12564946 0.12908779 0.125872025 0.138903092 0.07769753 0.151376143 0.13412026 0.06301572 0.016512014 0.143046925 0.060385229 0.09403300 0.09011466 1.000454e-01 0.06157109 0.0991045239 0.12279758 0.253940846 0.13568681 0.09514299 0.10352198 0.068370673 0.128229857 0.072290480 0.20559555 0.070210776
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> ## until the updated GSVAdata goes through the build system
> ## remove duplicated rows
> fnames <- featureNames(huangArrayRMAnoBatchCommon_eset)
> mask <- duplicated(fnames)
> huangArrayRMAnoBatchCommon_eset <- huangArrayRMAnoBatchCommon_eset[!mask, ]
> pickrellCountsArgonneCQNcommon_eset <- pickrellCountsArgonneCQNcommon_eset[!mask, ]
>
> 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)
> 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 0.21721983 0.18996785 0.20541802 0.21636999 0.228918711 0.20965435 0.22509442 0.2235649655 0.220977222 0.21472697 0.21916441 0.220872497 0.20929258 0.21025902 0.20503366 0.20002652 0.19737894 0.1915313816 0.225171727 0.21722501 0.20442539 0.201715078 0.19389845 0.23136672 0.2215222396 0.212502607 0.22812038 0.221224253 0.204353401 0.2189767209 0.222743312 0.229498351 0.22080396 0.20317828 0.21913890 0.215767375
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.32446168 0.33049406 0.31884595 0.30778040 0.322825961 0.31549239 0.31984749 0.3186253154 0.329884236 0.31286516 0.32686043 0.331932334 0.31520004 0.32292166 0.31033759 0.31226198 0.30735116 0.3169153941 0.320574586 0.32927871 0.31034821 0.313491489 0.32322380 0.32454467 0.3077295170 0.302026455 0.31443410 0.325026294 0.324331257 0.3207569835 0.313222653 0.322386067 0.32321091 0.31485179 0.32985610 0.323056595
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.32631340 0.29204422 0.32185699 0.31933707 0.327513824 0.32317246 0.31703064 0.3269409336 0.317967058 0.30574471 0.32082637 0.325425815 0.31570330 0.32224347 0.30440257 0.31213747 0.30065861 0.3175689706 0.313330007 0.31543774 0.31510779 0.312095463 0.31153241 0.31362242 0.3132282287 0.305566472 0.31325712 0.318608621 0.309384440 0.3169379532 0.307955239 0.319524108 0.30335555 0.31482507 0.31942853 0.327111509
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.14182627 0.15211647 0.14271965 0.07976681 0.105400252 0.13016198 0.11308442 0.1603923704 0.141745067 0.09916369 0.16442237 0.158782258 0.10833470 0.17684148 0.13426092 0.11420977 0.14198863 0.1430677974 0.147053335 0.14852317 0.17190386 0.138824792 0.12229741 0.11695718 0.1094203746 0.069661903 0.14073541 0.182091703 0.114802588 0.1892910845 0.130613078 0.111700323 0.14423809 0.12352402 0.12239871 0.138517034
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.15589670 0.11795124 0.14733246 0.18726742 0.200179743 0.16460420 0.16814668 0.1803802820 0.170651270 0.18705111 0.18269329 0.164689570 0.16802619 0.17156053 0.16624099 0.14549160 0.13417407 0.1380493809 0.169178867 0.19245515 0.19070812 0.157703935 0.12731027 0.18645181 0.1952875908 0.176668101 0.19832418 0.161645680 0.152215693 0.1738055901 0.187529032 0.197625166 0.17265418 0.16157298 0.17927827 0.180461216
KEGG_GALACTOSE_METABOLISM 0.11185015 0.10303851 0.11114710 0.13762911 0.166229899 0.14462814 0.12737125 0.1372223140 0.143127853 0.15288235 0.15242597 0.150015563 0.15025630 0.14641113 0.12005469 0.11583190 0.11616116 0.1150820655 0.149767286 0.16914156 0.16521804 0.123969626 0.09231554 0.14960607 0.1765509593 0.129242228 0.17104478 0.137921945 0.112938564 0.1399801929 0.144929790 0.159188497 0.13460516 0.12474294 0.15643452 0.170268454
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.04264010 -0.03231123 0.01452384 -0.01036832 -0.021910717 -0.03141318 -0.01011631 0.0665210061 -0.006902107 -0.02868722 0.01181211 0.001943343 -0.01396127 0.03484297 -0.03185196 -0.01755440 -0.01490230 -0.0023964829 0.027566134 -0.04844573 -0.11519624 -0.008424876 -0.01168678 -0.02052165 0.0009019816 -0.002966386 -0.11321544 0.027588713 -0.020395271 0.0504415468 0.024212180 0.004538288 0.02797590 -0.01407919 -0.01892488 0.007548007
KEGG_FATTY_ACID_METABOLISM 0.19183128 0.17744988 0.19250355 0.18184509 0.195341708 0.17331431 0.18747206 0.2096229722 0.189591529 0.17790897 0.17750849 0.187869753 0.17494495 0.18089300 0.17590931 0.16301176 0.17738479 0.1849919449 0.187438993 0.17632413 0.15161479 0.184412247 0.17559254 0.18563812 0.1645376075 0.179295725 0.15698821 0.189770625 0.183474439 0.1897408272 0.186139806 0.195803395 0.20428606 0.18329585 0.17999004 0.186395203
KEGG_STEROID_BIOSYNTHESIS 0.29524811 0.29529433 0.26305985 0.27916683 0.291369504 0.28611129 0.30488156 0.3029092157 0.306255676 0.26810882 0.29474406 0.281947459 0.28373972 0.30315304 0.30913403 0.26600805 0.26954889 0.3018917086 0.272501281 0.28932257 0.27874550 0.272988159 0.28296743 0.28604081 0.2974946694 0.264534612 0.26805495 0.276212036 0.286420777 0.3080208857 0.289250451 0.299843542 0.29282928 0.29953128 0.29475944 0.287624480
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS -0.03527686 -0.09206897 -0.04724951 0.05922845 -0.123040372 -0.08440223 -0.02247123 -0.0444895464 -0.063808673 -0.15011601 -0.07680543 -0.027420724 -0.03119158 -0.08959075 -0.12837025 -0.15420608 -0.15144271 -0.0006081975 -0.141766799 -0.12405389 -0.14911801 -0.051949731 -0.06070369 -0.03605965 -0.1464126356 -0.128765886 -0.15301862 0.017645099 0.013456000 0.0212309112 -0.008194779 -0.079071591 -0.01500256 -0.09495015 -0.12155351 -0.100440547
KEGG_STEROID_HORMONE_BIOSYNTHESIS -0.00557581 -0.04856694 -0.07962122 -0.01634905 -0.091044018 -0.04599868 -0.05768200 -0.0074510201 -0.032139943 -0.04874069 0.01286925 -0.026577359 -0.05129199 -0.03421180 -0.09091778 -0.04584484 -0.06287348 -0.0034919294 -0.083543200 -0.04389054 -0.07381303 -0.041702930 -0.06695905 -0.06192588 -0.0227702629 -0.063490224 -0.05022174 -0.046592348 -0.007548499 -0.0308809908 0.039232151 -0.057971384 0.01429542 -0.04122957 -0.10027592 -0.022232617
KEGG_OXIDATIVE_PHOSPHORYLATION 0.23497936 0.26556806 0.26354533 0.24733681 0.255381506 0.25170841 0.25458089 0.2568403676 0.246695570 0.25779092 0.25802374 0.247747022 0.25323279 0.26055543 0.24846320 0.24628500 0.25194750 0.2622938525 0.253222517 0.24479145 0.24463543 0.248384064 0.24603574 0.26103437 0.2524703309 0.259547718 0.25726942 0.244747666 0.244996475 0.2471416259 0.249469042 0.253249454 0.25628033 0.26143053 0.26144384 0.249062840
KEGG_PURINE_METABOLISM 0.11325584 0.11332828 0.13077673 0.12893752 0.130817932 0.12561449 0.12720947 0.1256873440 0.114700735 0.11788264 0.12747490 0.124280253 0.12512453 0.12946903 0.11873267 0.11061891 0.11863947 0.1308693330 0.121043210 0.11896563 0.12491349 0.118883839 0.11022199 0.12366477 0.1117663302 0.125384977 0.12630639 0.120610144 0.116815136 0.1210626033 0.125983950 0.120815453 0.12099075 0.12316753 0.11800994 0.119580506
KEGG_PYRIMIDINE_METABOLISM 0.17800387 0.17527065 0.19884535 0.19701890 0.184777785 0.18903706 0.19454189 0.1915954305 0.176950850 0.18800446 0.18769787 0.191255069 0.17718099 0.19361466 0.18615347 0.18077753 0.18542345 0.1964488373 0.174531528 0.18933558 0.18810401 0.175298859 0.17764859 0.19064730 0.1772305033 0.198975792 0.18500821 0.173320601 0.179735366 0.1736996771 0.177995754 0.185681551 0.19296710 0.19237550 0.17700142 0.185011599
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.11018091 0.09294768 0.09093082 0.09992257 0.110831140 0.08971302 0.10840243 0.1024259643 0.098931566 0.09485157 0.10432982 0.113144923 0.09856275 0.09881155 0.10840186 0.10220347 0.09481083 0.0891737271 0.115000274 0.12387476 0.09915763 0.096112403 0.08818501 0.11116253 0.1016561395 0.090437660 0.10035184 0.114025237 0.088853019 0.1119400206 0.102128997 0.091755227 0.08657544 0.10471612 0.09690680 0.114057430
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.07628668 0.01307178 0.03101003 0.05515989 0.075463953 0.04673004 0.05698317 0.0723469694 0.092114623 0.05565018 0.08771003 0.050476883 0.05982430 0.06093465 0.08411111 0.10257639 0.01534408 0.0049506028 0.049345045 0.07073074 0.05144714 0.045243833 0.05156095 0.06443263 0.0854631978 0.053141309 0.06161289 0.050620090 0.064627852 0.0692397313 0.068054801 0.075245655 0.03343401 0.05209816 0.09375715 0.070300250
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.25918823 0.22908633 0.23931943 0.24468764 0.251224655 0.23650854 0.24676096 0.2544249892 0.257027419 0.24181180 0.26158127 0.245785017 0.24380308 0.24911075 0.26862100 0.25537591 0.22958776 0.2350093908 0.238041909 0.24118880 0.26569055 0.234649830 0.23413561 0.23312136 0.2583443901 0.215868622 0.23487909 0.256747679 0.240069729 0.2503534031 0.237280277 0.252814643 0.22675799 0.23882384 0.25746678 0.244663768
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.18883424 0.18650551 0.17557638 0.15658617 0.178655772 0.18085341 0.18591447 0.1965965285 0.191986472 0.14239247 0.20175131 0.181876584 0.18804991 0.18232923 0.18887323 0.17039133 0.16977864 0.1678429938 0.183820453 0.19763988 0.16368082 0.161257462 0.15806295 0.18377007 0.1711229256 0.163882200 0.15084200 0.197174191 0.185732185 0.1982308514 0.174408250 0.182924303 0.17837675 0.16090692 0.19907645 0.190470297
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.28597966 0.28257466 0.24987352 0.24513138 0.270809700 0.29659978 0.25835465 0.2522956908 0.282009158 0.24763585 0.32062187 0.275069920 0.28305890 0.30041147 0.30306313 0.29139854 0.28285654 0.2580612581 0.267239527 0.32469106 0.29207908 0.267323752 0.24763192 0.28306454 0.2938935043 0.262322661 0.29456652 0.269466310 0.263418681 0.2668145469 0.261212111 0.251367355 0.25148998 0.28433772 0.31307106 0.299593259
KEGG_LYSINE_DEGRADATION 0.11407442 0.09382349 0.11782931 0.11941889 0.114473142 0.11464425 0.11389916 0.1284496058 0.110734405 0.10309803 0.10924074 0.120264909 0.11123369 0.09948345 0.10405039 0.09181117 0.11042324 0.0994052703 0.114472046 0.11125822 0.10546333 0.095505038 0.09685105 0.10334061 0.1086062981 0.114488680 0.09122678 0.108374699 0.111399195 0.1171784351 0.104032100 0.110409819 0.10448105 0.09261547 0.10754065 0.112386623
KEGG_ARGININE_AND_PROLINE_METABOLISM 0.12764946 0.12055210 0.12816676 0.12793214 0.140381579 0.11267991 0.13893640 0.1364776104 0.118545890 0.12529668 0.13403358 0.119966520 0.12679147 0.11430758 0.12770117 0.12067034 0.11125538 0.1062000915 0.135324575 0.11397563 0.11288549 0.120517853 0.10901776 0.13682578 0.1483193221 0.127679567 0.12056048 0.130073940 0.120173269 0.1435536666 0.139448087 0.139822706 0.12657002 0.12322466 0.13683535 0.130249707
KEGG_HISTIDINE_METABOLISM 0.01094636 -0.00936846 -0.02466989 -0.03984077 -0.003726944 -0.02847858 -0.02499903 0.0008721746 -0.015007978 -0.03171141 -0.03673702 -0.017681608 -0.04403008 -0.03539251 -0.02405048 -0.02933671 -0.02621412 -0.0312195354 0.009365323 -0.04673035 -0.06843640 -0.022694260 -0.03062155 -0.03676474 -0.0255030415 -0.039825198 -0.08617490 0.004277051 -0.029682747 -0.0003703405 -0.019976169 -0.027051070 -0.01093124 -0.03008042 -0.02124978 -0.035520407
KEGG_TYROSINE_METABOLISM 0.06753397 0.05290119 0.05770778 0.04349213 0.057272553 0.05836395 0.05858804 0.0509600740 0.058842036 0.04745176 0.05780087 0.046945575 0.04964383 0.06579719 0.07188325 0.05398455 0.05778994 0.0691937578 0.044447478 0.04366717 0.06340185 0.067264165 0.04899601 0.05360736 0.0526043668 0.041290409 0.04403640 0.064516224 0.055322021 0.0484423707 0.070088304 0.042856073 0.06603251 0.06558193 0.05869159 0.057652972
KEGG_PHENYLALANINE_METABOLISM 0.11963716 0.09622739 0.09466570 0.09056768 0.091218014 0.09184515 0.09985165 0.0975407386 0.104921261 0.08747543 0.09590836 0.092070748 0.10457927 0.09912605 0.10427463 0.10698595 0.07948661 0.0989468131 0.119134895 0.09914608 0.10452572 0.086232868 0.09680196 0.10514388 0.0976260981 0.085916976 0.09975787 0.107143882 0.084064813 0.0915211900 0.102144015 0.107409575 0.10266364 0.09500716 0.08808469 0.098433629
KEGG_TRYPTOPHAN_METABOLISM 0.12740929 0.13577138 0.12025881 0.10215757 0.105727984 0.10296569 0.11271988 0.1473129592 0.134446344 0.09439503 0.12408323 0.114771330 0.10218883 0.12975022 0.09530952 0.11916134 0.10779215 0.1239415799 0.126037527 0.11886633 0.06676474 0.112630341 0.11228894 0.10030582 0.1180285091 0.113713721 0.09177254 0.132651298 0.110507418 0.1204234839 0.125432246 0.116328296 0.14711772 0.12007138 0.10448497 0.118966894
> pickrellPar <- ssgseaParam(pickrellCountsArgonneCQNcommon_eset,
+ canonicalC2BroadSets, minSize=5, maxSize=500)
> esrnaseq <- gsva(pickrellPar, verbose=FALSE)
> 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 0.255973871 0.234244836 0.22340103 0.25147113 0.25604502 0.22418622 0.26808957 0.24342921 0.22291266 0.24434352 0.241461667 0.24764348 0.240706877 0.26427645 0.25153628 0.221695112 0.25933664 0.257579414 0.237132544 0.23355947 0.24083186 0.24377961 0.24398934 0.253362819 0.229899549 0.232863910 0.25288826 0.25070805 0.2350691397 0.25292904 0.25386372 0.23975752 0.23464696 0.24542300 0.25626878 0.25051771
KEGG_CITRATE_CYCLE_TCA_CYCLE 0.276721079 0.263644751 0.24671314 0.27511916 0.27544540 0.24952920 0.28813898 0.26719607 0.22432070 0.25808503 0.264374411 0.26609297 0.267760618 0.27281530 0.26932935 0.218624667 0.28127101 0.273970441 0.253553333 0.25911760 0.26054107 0.26844807 0.27055856 0.265170337 0.243920672 0.241108955 0.28510006 0.28097655 0.2407076495 0.26191338 0.26220803 0.27378757 0.25408726 0.26875884 0.27358412 0.26446288
KEGG_PENTOSE_PHOSPHATE_PATHWAY 0.308020808 0.297901469 0.28989411 0.31299315 0.31062622 0.29557813 0.33138058 0.30891326 0.27198469 0.29291718 0.318217559 0.31734453 0.303133878 0.32976745 0.31585270 0.275896528 0.32122060 0.328762461 0.288492608 0.28968383 0.29747578 0.29393201 0.30385264 0.308813494 0.284093229 0.286685677 0.32273350 0.31658653 0.2937498126 0.30270973 0.30274210 0.30105302 0.29975257 0.30855189 0.29564512 0.31094443
KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS 0.072490776 0.057665424 0.05042026 0.05497896 0.06838128 0.07721215 0.08165341 0.09208236 0.03505170 0.09123428 0.097520413 0.06906502 0.081204820 0.14558660 0.10070838 0.031256469 0.09159758 0.115363944 0.088310700 0.08098270 0.11279059 0.04548519 0.05879566 0.091246266 0.044849846 0.014590393 0.11201919 0.13581918 0.0576718138 0.07863358 0.10737231 0.06168125 0.10049004 0.07836096 0.04773881 0.08027239
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 0.178853698 0.181117241 0.18127676 0.20618109 0.16474691 0.15651927 0.20496583 0.18186585 0.12796430 0.18919793 0.194352045 0.18648633 0.191330063 0.18583711 0.21655450 0.163603168 0.20121985 0.213403292 0.170896337 0.18299748 0.17715740 0.18020032 0.18630756 0.208329171 0.182319139 0.186208415 0.20214840 0.14286122 0.1689044226 0.17558507 0.20034137 0.16248263 0.16171966 0.19872350 0.18448376 0.20468815
KEGG_GALACTOSE_METABOLISM 0.180866571 0.159543878 0.16227291 0.20539900 0.18018335 0.15498483 0.21922691 0.17807913 0.12333373 0.18313170 0.198801246 0.19418260 0.190226610 0.19518870 0.22219754 0.149177439 0.20534732 0.200288866 0.169905819 0.18195222 0.18920139 0.17577461 0.16963025 0.194575390 0.198051080 0.192049056 0.22210179 0.15370205 0.1631961787 0.17220540 0.20561062 0.15856520 0.15381957 0.18863664 0.18887519 0.20809743
KEGG_ASCORBATE_AND_ALDARATE_METABOLISM 0.075839356 0.079870770 0.01839691 0.05295801 0.05594010 0.03619848 0.08085292 0.05211813 0.02046458 0.09556844 0.045945102 0.03536734 0.072302956 0.13924114 0.04048614 0.000868274 0.08528874 0.108627906 0.054713382 0.01778929 -0.08069455 0.01882544 0.06240893 0.065481911 0.023139332 0.006485666 0.03032984 0.10225397 -0.0037549053 0.05275949 0.07459863 0.08237901 0.05589809 0.04198289 0.06239312 0.07388409
KEGG_FATTY_ACID_METABOLISM 0.189545892 0.170487970 0.14107909 0.19152027 0.20036184 0.16180871 0.20687596 0.18054223 0.16653839 0.17649890 0.168908518 0.17875348 0.178533717 0.20967324 0.17159817 0.130611489 0.20904897 0.197016502 0.164712821 0.15795025 0.16354191 0.17822402 0.18280684 0.187852572 0.113071322 0.130261054 0.17735453 0.19431706 0.1593913401 0.18846504 0.18883700 0.18933507 0.15945060 0.16646827 0.17874163 0.19724564
KEGG_STEROID_BIOSYNTHESIS 0.224203013 0.183303179 0.10596218 0.15398123 0.20660401 0.19357323 0.19895056 0.19354072 0.13738963 0.13250921 0.166087855 0.15449865 0.201680501 0.18416480 0.20216814 0.138593021 0.16130884 0.187533552 0.127409131 0.17258652 0.17184479 0.17658992 0.20496232 0.178032960 0.221859949 0.187127542 0.17884508 0.15830785 0.1559615607 0.17949533 0.21176210 0.18619753 0.20543338 0.21969290 0.24219179 0.17351891
KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS 0.006756532 -0.045782593 -0.05681410 0.07110818 -0.03839128 -0.06537417 -0.01691239 -0.01174482 -0.07123455 -0.07226010 -0.041041770 -0.01482012 0.004425068 0.04992665 -0.04779878 -0.071089965 -0.04307171 -0.017284164 -0.035488641 -0.06358435 -0.04624196 -0.03151707 -0.02267855 -0.004022051 -0.083034638 -0.065514503 -0.04784385 -0.03744402 -0.0005655492 0.03696114 0.04582892 -0.02683713 -0.04880944 -0.05773766 -0.04101500 -0.03689178
KEGG_STEROID_HORMONE_BIOSYNTHESIS -0.046658311 -0.094049506 -0.13823804 -0.05907553 -0.11515098 -0.04435061 -0.07844386 -0.07347585 -0.10065156 -0.06042842 -0.052315196 -0.07130284 -0.082016425 -0.04890030 -0.08818966 -0.080981150 -0.09427154 -0.072991221 -0.132047304 -0.06463561 -0.13630508 -0.09083536 -0.11657925 -0.086356880 -0.095038994 -0.120331272 -0.07225945 -0.03510727 -0.0668165610 -0.10586318 0.02671161 -0.04934596 -0.05349457 -0.11643009 -0.12958753 -0.06607392
KEGG_OXIDATIVE_PHOSPHORYLATION 0.289875603 0.306180274 0.26008466 0.29541751 0.29439500 0.28659621 0.31500729 0.29204880 0.29611294 0.28171311 0.288757552 0.29818332 0.295881714 0.30697427 0.29386532 0.297765229 0.29571081 0.303990507 0.280545983 0.28709475 0.29820052 0.30086013 0.29124721 0.294101932 0.251997289 0.264215516 0.29632865 0.30623682 0.3065889480 0.28923030 0.30193543 0.30177690 0.31174532 0.28598468 0.28879303 0.28703293
KEGG_PURINE_METABOLISM 0.121199616 0.113729580 0.11003028 0.13065417 0.11798635 0.10826198 0.12913892 0.12009178 0.08407076 0.11195380 0.112481215 0.11494730 0.105008038 0.13116526 0.11960315 0.112557873 0.12856140 0.122682619 0.119374712 0.10548339 0.10871674 0.11069066 0.10468173 0.108918495 0.098684948 0.102537595 0.12680997 0.13711068 0.1139065356 0.12013213 0.10935277 0.11335705 0.10240861 0.11724310 0.10688270 0.11146964
KEGG_PYRIMIDINE_METABOLISM 0.159364219 0.145034413 0.14683938 0.17367689 0.15303132 0.14746795 0.16815099 0.15853649 0.11338321 0.15119996 0.146658541 0.15150584 0.126621736 0.17142933 0.15824172 0.142391725 0.16265716 0.161071263 0.147383996 0.14114834 0.14627424 0.14142842 0.14494780 0.146013445 0.114023679 0.130659164 0.16539603 0.18053868 0.1511483017 0.16018537 0.13583283 0.16226122 0.13939515 0.15512501 0.13584431 0.15347271
KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM 0.112508883 0.074202209 0.08660117 0.09207883 0.11280671 0.09472827 0.09704054 0.07733135 0.10943575 0.07564145 0.076565645 0.07899580 0.081264824 0.10757013 0.09734334 0.046542835 0.08917489 0.076487510 0.091295210 0.07796498 0.07171296 0.08706823 0.06550663 0.087144765 0.072742315 0.070136832 0.10741914 0.09203473 0.0631336245 0.12192789 0.08543094 0.06735452 0.05914758 0.07996024 0.08585010 0.09660417
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM 0.063066152 0.008244582 0.05888892 0.06656162 0.06755857 0.04379612 0.03310672 0.04702300 0.07188416 0.04974758 0.019198599 0.05230415 0.007011605 0.07932181 0.04631052 0.006101109 0.03600723 0.007179737 0.059641322 0.01372905 -0.02144312 0.04741604 0.03671989 0.033030921 0.058596958 0.025885885 0.05314484 -0.01905521 0.0344527035 0.09811477 0.03587761 0.02208787 -0.01476052 0.03810409 0.09572419 0.07020138
KEGG_CYSTEINE_AND_METHIONINE_METABOLISM 0.233841890 0.189564988 0.20507257 0.22829497 0.22708184 0.19891652 0.19829674 0.22080930 0.21841648 0.21549322 0.192090772 0.19635785 0.202624437 0.24415962 0.22573236 0.162311561 0.19762888 0.190417790 0.196717053 0.18142032 0.20830986 0.21357824 0.20096179 0.201421602 0.211807543 0.203022494 0.19715210 0.19397219 0.1831123581 0.22839547 0.18688488 0.20420093 0.17810573 0.19787799 0.21869417 0.22013221
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION 0.149451223 0.130390435 0.11090077 0.15171054 0.15674850 0.12207153 0.17676341 0.13240117 0.14595322 0.12775620 0.154294491 0.13844160 0.147993017 0.18547995 0.14445481 0.099906770 0.16080600 0.158214170 0.127978549 0.13338533 0.12794009 0.13430359 0.13380999 0.163421828 0.097145942 0.107391342 0.15045297 0.15959356 0.1167283443 0.15777718 0.14485771 0.14543148 0.13887590 0.12885753 0.15223409 0.15723079
KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS 0.295049854 0.261601594 0.20403465 0.28738325 0.29603089 0.27196679 0.27622279 0.24595352 0.27911628 0.21938983 0.291009359 0.26240936 0.257169673 0.29805967 0.28918494 0.233479253 0.27807435 0.255999607 0.243017519 0.27438415 0.27711754 0.24764661 0.23187567 0.282690377 0.269031146 0.250755848 0.30790395 0.28484647 0.2548749648 0.27333689 0.26646895 0.24028977 0.27659068 0.24372431 0.28254069 0.28445791
KEGG_LYSINE_DEGRADATION 0.141445452 0.125002226 0.13255242 0.14247800 0.13445308 0.12163080 0.14683973 0.13350430 0.09455978 0.12203523 0.121846397 0.12672657 0.124437291 0.13792739 0.13711666 0.119280133 0.14191460 0.133529312 0.143966681 0.11140711 0.10524696 0.13044997 0.13773078 0.134887830 0.112264818 0.122763552 0.12934023 0.13530622 0.1228715577 0.13550145 0.12430132 0.13593479 0.10488655 0.13490541 0.13528939 0.14122687
KEGG_ARGININE_AND_PROLINE_METABOLISM 0.135482923 0.122800947 0.10546760 0.12529070 0.14881835 0.11780892 0.13985852 0.12241508 0.09404450 0.11735467 0.139880299 0.10924993 0.124094947 0.13132972 0.12119785 0.089756673 0.12963747 0.126783881 0.117471694 0.11395978 0.11733101 0.13675663 0.11316903 0.130174672 0.104091634 0.117336202 0.12537136 0.11143364 0.1056317091 0.14603708 0.13290068 0.10604271 0.10926022 0.12441688 0.14465486 0.12962314
KEGG_HISTIDINE_METABOLISM -0.031406167 -0.027028114 -0.05320652 -0.03884676 -0.03768201 -0.05311762 -0.03059749 -0.04403581 -0.04575910 -0.02307710 -0.069587330 -0.05100703 -0.063814721 -0.02769063 -0.05394060 -0.064034876 -0.03240874 -0.040189433 -0.028223850 -0.04656494 -0.06820722 -0.03735737 -0.02600696 -0.040982550 -0.045504413 -0.058399118 -0.06855384 -0.02182960 -0.0482012289 -0.03138879 -0.03374364 -0.03833469 -0.04428041 -0.03169806 -0.01319006 -0.03962329
KEGG_TYROSINE_METABOLISM 0.017084992 0.013181478 0.01268639 0.04713214 0.01176082 0.02979957 0.04417175 0.03403665 0.01332206 0.03659289 0.022255722 0.02675872 0.009888131 0.04903079 0.03012079 0.023843052 0.04643905 0.039686340 0.009885306 0.02695262 0.03836951 0.04709984 0.02558438 0.038489611 -0.012243132 0.006588370 0.04123095 0.02120107 0.0534860072 0.02777202 0.04696405 0.02599549 0.05481278 0.01839159 0.06080289 0.03592215
KEGG_PHENYLALANINE_METABOLISM 0.039223065 0.029140116 0.02737110 0.04131291 0.02543846 0.04082318 0.02604365 0.04681683 0.04448473 0.02668485 0.009443264 0.01801024 0.029907958 0.06543161 0.04981445 0.029020563 0.03200465 0.037690432 0.045323751 0.01243177 0.07294275 0.05536484 0.05322965 0.038324553 0.006928568 0.043245725 0.05273879 0.02880029 0.0305594156 0.04343878 0.06363048 0.02883049 0.02467284 0.04462306 0.06299359 0.01967917
KEGG_TRYPTOPHAN_METABOLISM 0.123047327 0.122664093 0.07570663 0.11492944 0.10828508 0.10297933 0.12667410 0.12674000 0.09130083 0.10170316 0.117485972 0.11432743 0.106990443 0.13120525 0.10417994 0.095119597 0.11195818 0.118766135 0.109696728 0.09143247 0.07791307 0.11149700 0.12123200 0.101461411 0.088796360 0.080136676 0.11191365 0.15854422 0.0951832300 0.11281184 0.12597991 0.13622521 0.12241147 0.10750563 0.12420200 0.11243731
>
> 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)
> 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 Under development (unstable) (2024-11-14 r87333) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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>
> ## 2024-10-25 regression test script for method z-score
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2024-10-25)
> 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 1.1025783 -0.9348073 1.2604604 -0.5213579 -0.1449497
g2 1.1178965 -1.1697762 -0.6188039 -1.5167080 -1.1104456
g3 -1.8181019 -1.1516529 0.9891236 -1.0173901 0.7009874
g4 -0.1944140 -0.3479166 -0.7471371 -0.6796938 1.5027270
g5 -0.6131956 1.0524922 -0.5313147 0.6119898 0.3619898
> 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 -1.06458048 -0.83018864 -0.22242444 0.01770907 1.29572900 1.08479219 -0.2026341 0.09528427 0.6043784 1.06106883 0.18149233 -0.20380902 0.974460339 -1.0840869 1.014299379 1.24553781 0.27796592 -0.74192975 -0.15737684 -0.44433957 -2.16672220 -0.90971035 0.71456752 0.45472286 1.67857540 -1.20167956 -0.0030951 0.67108139 -2.4230727 0.28398504
gs2 0.70441952 -1.06923399 -0.74409554 1.02432776 1.24402969 -0.40917297 0.7260839 0.89511331 0.5612332 1.80006170 -0.18964254 0.14204149 -0.776263017 -0.9886871 0.603511795 -0.42171397 -0.04741470 -0.65211191 2.06021093 -0.06610576 0.06756050 -0.44991411 -1.06881951 -0.52695079 -0.02748786 -0.88341535 0.2187851 -0.35953570 -0.5148857 -0.85192837
gs3 0.88524637 -0.71355486 0.90816597 0.06155735 -0.39427798 1.18031034 1.4612057 0.11078573 -0.2152689 -0.42469059 0.57424369 0.28620777 -0.873367098 -0.1313144 0.651697918 -0.18027739 -0.08015365 0.99384177 -0.40720257 -0.86162107 -0.30480539 -0.30109857 -0.54375718 -0.23434002 -0.80526649 -0.61444389 0.8800897 -0.28527193 -0.5808800 -0.04176029
gs4 0.13541837 -0.35479268 -0.61750996 -1.29885188 -0.54186586 1.81953254 0.8450039 -0.91632112 1.4749560 0.91732846 -0.94339946 -1.08992196 0.874047020 -0.7023891 -1.056552454 1.19898288 0.62893663 -0.67200929 1.50611676 -0.58482114 0.47882851 -0.49083324 0.49889537 -0.39605406 -1.78332955 0.53510025 0.3105174 -0.71771181 0.3835326 0.55916680
gs5 0.71901829 0.09732103 2.01875411 1.69987635 -0.48206837 0.99560408 -1.8962627 1.42523254 -0.2918237 0.33479500 -0.09539723 0.87713599 -0.624674373 -0.1608037 -0.533916027 -1.11781585 -0.81779029 -1.54380038 -0.40693090 0.58246572 1.75724228 0.09642816 1.24313304 0.28685300 -0.59748181 -0.18950558 0.4777956 -0.66708105 -3.3157979 0.12949462
gs6 1.35271991 0.63749510 -0.61083911 0.31960250 1.22397884 -0.05050125 -2.1271341 1.28249345 0.1162182 -0.37886000 1.14434446 0.88555219 -0.228806622 -1.0308073 -0.565274938 -0.52668413 -0.54182481 -0.88788234 0.27604113 0.42414614 0.31362703 -0.54651013 -1.35247175 1.37303938 0.58905340 -0.30839738 -0.6320409 0.05918995 0.7819692 -0.99143612
gs7 0.96674977 -0.93294321 0.56410159 -0.21620985 0.06088514 0.96849397 1.4523929 -1.03861548 1.1168251 -0.55796726 -0.16453933 -1.43702530 -0.166746577 -1.1616513 0.207972961 -0.64135154 -0.85568268 -0.94201976 0.81963981 -0.48286792 -0.61340630 1.74139964 -0.77655843 0.57059179 0.58690407 0.99599130 -0.2610899 -0.49130603 -1.1458303 1.83386325
gs8 -0.32073030 0.82199558 -0.35071681 -1.08557202 -0.84898763 -0.20063755 -0.9860735 1.86438708 1.0749257 0.20951029 0.92927439 -0.93001532 0.007357371 1.1451471 -1.532132408 -1.04980179 0.86798842 -0.30736768 0.82896829 -0.39046106 0.95339305 1.41402387 0.67899334 -1.85289118 -0.79025269 -0.06148920 -0.3960239 0.59994668 0.6722927 -0.96505071
gs9 -0.97848220 -1.93158002 -0.57963554 -0.88363639 -0.38238739 -1.01845126 0.8962102 -1.50386283 0.6264871 -0.98580129 0.89760495 -0.71235491 0.780787018 -1.1613036 0.676283580 -0.67542347 -0.57888323 -1.63104361 0.68701922 0.66109300 0.37150042 -0.09226790 0.99472003 0.30434233 -0.28849234 0.27079674 1.4658920 0.31250388 1.0632598 3.39510566
gs10 -1.73619631 0.50147856 1.14009382 -0.80323502 0.33383762 -0.94997427 1.3169210 -0.23896633 -1.0607943 0.87257852 -0.72309883 0.06789371 -2.293490442 -0.9441776 0.423682194 0.38483730 -1.72241801 1.19597278 -0.60768058 0.21350397 -0.27929805 0.70694350 -1.64987791 0.97067127 0.67707419 1.56497170 0.5122503 1.20859132 0.5868649 0.33104098
gs11 0.81881266 1.31471412 -1.09252898 0.25427732 0.21262415 0.83249830 -1.5308017 -1.11166915 0.4880360 1.08643673 -1.01432635 -0.62026388 -0.557310545 -1.0075568 1.853018012 -0.37055173 0.69001473 0.45100377 0.24653759 -1.19952724 0.09593994 0.32663248 -0.61940479 0.04655919 0.98856234 -2.04525229 -0.7036338 -0.10019437 0.4166058 1.85074853
gs12 -1.10054447 0.22063891 -1.37053429 -1.76446304 0.22800083 1.12716989 0.4224829 -0.91724368 0.5300894 -0.34597979 -1.18436938 0.57050211 -0.562600950 0.3020143 -0.705090642 0.24943201 0.82677721 -0.92927884 -0.31931554 0.32027301 -0.11594306 -0.36391081 0.25982674 0.41533281 0.99781911 -0.12991115 0.8217321 0.71462178 1.2330765 0.56939591
gs13 0.63928323 -1.52045285 0.06768295 0.06057797 -1.55253678 -0.52658435 1.8134009 0.91493040 0.8152034 -0.42649524 -0.47565066 -0.42380883 0.816345111 0.6640350 -0.253816915 -1.15087060 1.29036507 -0.05361272 0.13918266 0.61211781 -1.10297713 1.09084062 0.82571551 -1.96601152 -2.07805569 -0.50201699 0.7800126 1.07981894 0.6887845 -0.26540647
gs14 -1.12269002 -0.87867194 1.62060278 0.72970240 -0.40210659 -0.25307414 0.4584524 0.80621597 -0.6313727 -0.36976649 -0.18398081 -0.57687961 -1.969222861 0.1450684 -1.109488757 0.83901970 0.27820952 -0.80056753 -0.06316926 0.33606434 1.14421601 -0.55297018 0.37159450 0.29270793 -0.38185262 0.49290283 1.1747644 -0.36100438 -0.2073222 1.17461893
gs15 -0.80302615 -1.08916414 -0.50859099 0.75307944 -1.09261336 1.32515326 0.5759085 -0.05153603 -0.0874252 0.04977655 1.18504060 1.47109757 -1.018871841 -0.6702209 1.325561772 0.50928749 -1.64973582 0.24100292 1.27891287 -1.63005314 -0.81094245 0.11400053 0.35524453 1.93340273 -0.66480758 -0.13402365 -0.5497420 -0.65437128 -0.2106793 0.50833502
gs16 -0.49794597 0.11173796 -0.25559084 0.22339202 -0.64200232 -1.06027171 -0.2890369 1.19556001 -0.4032416 1.25356657 0.17652910 -0.19476214 1.266689482 -0.1247642 -0.559948207 -0.01704689 -0.72464431 -2.20081384 -0.15376113 -1.85192168 -0.07973415 -1.16618073 0.91452163 -1.01623802 -0.53633071 0.65478475 1.3545217 1.67222330 1.3510851 1.59962370
gs17 -0.09192484 -0.81489259 0.44113992 1.50083666 0.02989752 -0.07702809 1.1216086 -0.58155914 -1.0886995 -0.73736123 -0.32942151 -0.04370937 0.314676528 0.9820022 -0.208601981 -1.16796258 -0.67938471 -2.70665603 -0.77318960 1.15353807 2.12147238 0.58452002 0.02454425 1.82856706 1.65015182 -1.15785073 0.3546658 -0.34445966 -1.0254307 -0.27948863
gs18 -0.31852173 0.12067183 -1.25950009 0.76892943 0.46096286 -0.26662836 0.4417647 0.79129254 -1.9726560 0.43035752 0.45698355 -0.29005193 -1.813833043 0.3629808 0.236509319 -1.42021611 -1.05453320 1.41161896 1.36173027 0.77494149 0.84023752 0.38901914 0.95885634 -0.50800307 -0.67393504 -0.48992210 0.7004933 1.31021998 -0.6332057 -1.11656327
gs19 0.72641579 -0.57769847 0.49329687 -0.51183227 -1.11400559 0.64877026 -0.4406262 0.25071309 2.1136039 -0.52679579 -2.43932744 0.77103343 0.910888191 -0.9678455 -0.009019031 -0.62004911 0.32332812 1.08838097 -0.12574913 -1.57352212 -0.59724213 1.14917069 0.80924032 0.92711227 1.00116247 -0.06280573 1.2499995 -0.85619615 -1.1394307 -0.90097052
gs20 -0.40686085 -0.19758125 -0.45781926 -0.55886885 -0.12951342 -0.54918118 -1.4879999 0.82768742 1.1492282 0.52844266 0.52775384 -0.40217918 1.624947601 0.2093448 -0.333895058 0.11284783 2.10468712 -1.29927604 -1.42891137 -0.32736265 1.53004416 0.70793130 0.01872158 1.27121937 -0.41694874 -1.75501137 0.7076323 0.34166052 -2.2272134 0.31647390
gs21 0.11064959 0.63071460 -0.09315791 0.73101162 -1.00749109 -0.53271009 0.2591944 1.13172316 0.1506891 -0.87646695 -1.69439296 0.83702971 1.876937011 1.4478442 0.482520953 -1.29624843 0.76274193 0.01335892 0.67731457 -1.29116635 0.12279982 -0.42496995 -0.69988173 0.61045071 1.12362505 -0.26701006 -0.9392599 -0.83744301 0.2756659 -1.28407286
gs22 1.69743076 -0.62568897 0.95318018 0.79835944 -0.22877959 -0.33245259 -0.8818449 -0.07048306 0.3842529 0.59890023 1.19876650 0.89702407 -0.063815196 0.1767625 -0.247788166 -0.12757217 -0.78058894 -1.35990624 0.57884316 -0.32914348 -1.97746404 -0.96013904 -2.12070233 -0.60051457 0.51066179 0.92360209 1.2892500 -0.50402715 0.2956685 0.90820836
gs23 0.60506926 0.44111596 -1.65790604 -1.19005302 -1.63334726 1.91345338 0.1927653 -0.63878889 0.5837665 1.18492028 -0.46232575 -1.20423315 -0.218426414 -0.3260477 0.028282249 -0.12215401 -0.65082403 -0.57846899 0.78152042 0.48778655 0.95493242 -0.81023527 -0.15048463 1.44187787 0.77550222 0.23753821 -1.3126729 1.58523096 -0.4605529 0.20275941
gs24 -0.72148839 -0.54576956 -1.18688036 0.89207321 1.69203360 1.73911075 0.9927791 0.68541378 -0.1858115 -0.67635067 -0.95993033 -1.11607732 0.647530634 -0.7736508 -0.323911174 0.09530263 -0.01217018 0.24474840 1.24467781 0.01803482 -0.25900876 0.65090463 -1.30503212 -2.43406616 0.67009734 0.97148066 0.2259098 -0.36238688 1.8322860 -1.73984886
gs25 0.18453756 -1.41154192 1.23729871 0.79812134 0.08096990 -0.28095732 0.5439363 0.76789568 -0.5449132 1.23698241 0.43459496 -0.96638207 -1.685807242 0.3305633 -0.725234936 -0.20714446 -0.66613185 -0.41593820 -1.07617312 -0.64173119 0.11884874 2.77574824 0.54647524 -0.11517645 0.01675019 -0.66013610 0.1421437 -0.20674328 1.0131497 -0.62400460
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> ## until the updated GSVAdata goes through the build system
> ## remove duplicated rows
> fnames <- featureNames(huangArrayRMAnoBatchCommon_eset)
> mask <- duplicated(fnames)
> huangArrayRMAnoBatchCommon_eset <- huangArrayRMAnoBatchCommon_eset[!mask, ]
> pickrellCountsArgonneCQNcommon_eset <- pickrellCountsArgonneCQNcommon_eset[!mask, ]
>
> 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)
> 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)
> 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)
> 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
31.708 1.291 32.983
GSVA.Rcheck/tests/test_zscore_newapi.Rout.save
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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>
> ## 2024-10-25 regression test script for method z-score
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(commonPickrellHuang)
> data(genderGenesEntrez)
> data(gbm_VerhaakEtAl)
> data(brainTxDbSets)
> data(leukemia)
>
> set.seed(2024-10-25)
> 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 1.1025783 -0.9348073 1.2604604 -0.5213579 -0.1449497
g2 1.1178965 -1.1697762 -0.6188039 -1.5167080 -1.1104456
g3 -1.8181019 -1.1516529 0.9891236 -1.0173901 0.7009874
g4 -0.1944140 -0.3479166 -0.7471371 -0.6796938 1.5027270
g5 -0.6131956 1.0524922 -0.5313147 0.6119898 0.3619898
> 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 -1.06458048 -0.83018864 -0.22242444 0.01770907 1.29572900 1.08479219 -0.2026341 0.09528427 0.6043784 1.06106883 0.18149233 -0.20380902 0.974460339 -1.0840869 1.014299379 1.24553781 0.27796592 -0.74192975 -0.15737684 -0.44433957 -2.16672220 -0.90971035 0.71456752 0.45472286 1.67857540 -1.20167956 -0.0030951 0.67108139 -2.4230727 0.28398504
gs2 0.70441952 -1.06923399 -0.74409554 1.02432776 1.24402969 -0.40917297 0.7260839 0.89511331 0.5612332 1.80006170 -0.18964254 0.14204149 -0.776263017 -0.9886871 0.603511795 -0.42171397 -0.04741470 -0.65211191 2.06021093 -0.06610576 0.06756050 -0.44991411 -1.06881951 -0.52695079 -0.02748786 -0.88341535 0.2187851 -0.35953570 -0.5148857 -0.85192837
gs3 0.88524637 -0.71355486 0.90816597 0.06155735 -0.39427798 1.18031034 1.4612057 0.11078573 -0.2152689 -0.42469059 0.57424369 0.28620777 -0.873367098 -0.1313144 0.651697918 -0.18027739 -0.08015365 0.99384177 -0.40720257 -0.86162107 -0.30480539 -0.30109857 -0.54375718 -0.23434002 -0.80526649 -0.61444389 0.8800897 -0.28527193 -0.5808800 -0.04176029
gs4 0.13541837 -0.35479268 -0.61750996 -1.29885188 -0.54186586 1.81953254 0.8450039 -0.91632112 1.4749560 0.91732846 -0.94339946 -1.08992196 0.874047020 -0.7023891 -1.056552454 1.19898288 0.62893663 -0.67200929 1.50611676 -0.58482114 0.47882851 -0.49083324 0.49889537 -0.39605406 -1.78332955 0.53510025 0.3105174 -0.71771181 0.3835326 0.55916680
gs5 0.71901829 0.09732103 2.01875411 1.69987635 -0.48206837 0.99560408 -1.8962627 1.42523254 -0.2918237 0.33479500 -0.09539723 0.87713599 -0.624674373 -0.1608037 -0.533916027 -1.11781585 -0.81779029 -1.54380038 -0.40693090 0.58246572 1.75724228 0.09642816 1.24313304 0.28685300 -0.59748181 -0.18950558 0.4777956 -0.66708105 -3.3157979 0.12949462
gs6 1.35271991 0.63749510 -0.61083911 0.31960250 1.22397884 -0.05050125 -2.1271341 1.28249345 0.1162182 -0.37886000 1.14434446 0.88555219 -0.228806622 -1.0308073 -0.565274938 -0.52668413 -0.54182481 -0.88788234 0.27604113 0.42414614 0.31362703 -0.54651013 -1.35247175 1.37303938 0.58905340 -0.30839738 -0.6320409 0.05918995 0.7819692 -0.99143612
gs7 0.96674977 -0.93294321 0.56410159 -0.21620985 0.06088514 0.96849397 1.4523929 -1.03861548 1.1168251 -0.55796726 -0.16453933 -1.43702530 -0.166746577 -1.1616513 0.207972961 -0.64135154 -0.85568268 -0.94201976 0.81963981 -0.48286792 -0.61340630 1.74139964 -0.77655843 0.57059179 0.58690407 0.99599130 -0.2610899 -0.49130603 -1.1458303 1.83386325
gs8 -0.32073030 0.82199558 -0.35071681 -1.08557202 -0.84898763 -0.20063755 -0.9860735 1.86438708 1.0749257 0.20951029 0.92927439 -0.93001532 0.007357371 1.1451471 -1.532132408 -1.04980179 0.86798842 -0.30736768 0.82896829 -0.39046106 0.95339305 1.41402387 0.67899334 -1.85289118 -0.79025269 -0.06148920 -0.3960239 0.59994668 0.6722927 -0.96505071
gs9 -0.97848220 -1.93158002 -0.57963554 -0.88363639 -0.38238739 -1.01845126 0.8962102 -1.50386283 0.6264871 -0.98580129 0.89760495 -0.71235491 0.780787018 -1.1613036 0.676283580 -0.67542347 -0.57888323 -1.63104361 0.68701922 0.66109300 0.37150042 -0.09226790 0.99472003 0.30434233 -0.28849234 0.27079674 1.4658920 0.31250388 1.0632598 3.39510566
gs10 -1.73619631 0.50147856 1.14009382 -0.80323502 0.33383762 -0.94997427 1.3169210 -0.23896633 -1.0607943 0.87257852 -0.72309883 0.06789371 -2.293490442 -0.9441776 0.423682194 0.38483730 -1.72241801 1.19597278 -0.60768058 0.21350397 -0.27929805 0.70694350 -1.64987791 0.97067127 0.67707419 1.56497170 0.5122503 1.20859132 0.5868649 0.33104098
gs11 0.81881266 1.31471412 -1.09252898 0.25427732 0.21262415 0.83249830 -1.5308017 -1.11166915 0.4880360 1.08643673 -1.01432635 -0.62026388 -0.557310545 -1.0075568 1.853018012 -0.37055173 0.69001473 0.45100377 0.24653759 -1.19952724 0.09593994 0.32663248 -0.61940479 0.04655919 0.98856234 -2.04525229 -0.7036338 -0.10019437 0.4166058 1.85074853
gs12 -1.10054447 0.22063891 -1.37053429 -1.76446304 0.22800083 1.12716989 0.4224829 -0.91724368 0.5300894 -0.34597979 -1.18436938 0.57050211 -0.562600950 0.3020143 -0.705090642 0.24943201 0.82677721 -0.92927884 -0.31931554 0.32027301 -0.11594306 -0.36391081 0.25982674 0.41533281 0.99781911 -0.12991115 0.8217321 0.71462178 1.2330765 0.56939591
gs13 0.63928323 -1.52045285 0.06768295 0.06057797 -1.55253678 -0.52658435 1.8134009 0.91493040 0.8152034 -0.42649524 -0.47565066 -0.42380883 0.816345111 0.6640350 -0.253816915 -1.15087060 1.29036507 -0.05361272 0.13918266 0.61211781 -1.10297713 1.09084062 0.82571551 -1.96601152 -2.07805569 -0.50201699 0.7800126 1.07981894 0.6887845 -0.26540647
gs14 -1.12269002 -0.87867194 1.62060278 0.72970240 -0.40210659 -0.25307414 0.4584524 0.80621597 -0.6313727 -0.36976649 -0.18398081 -0.57687961 -1.969222861 0.1450684 -1.109488757 0.83901970 0.27820952 -0.80056753 -0.06316926 0.33606434 1.14421601 -0.55297018 0.37159450 0.29270793 -0.38185262 0.49290283 1.1747644 -0.36100438 -0.2073222 1.17461893
gs15 -0.80302615 -1.08916414 -0.50859099 0.75307944 -1.09261336 1.32515326 0.5759085 -0.05153603 -0.0874252 0.04977655 1.18504060 1.47109757 -1.018871841 -0.6702209 1.325561772 0.50928749 -1.64973582 0.24100292 1.27891287 -1.63005314 -0.81094245 0.11400053 0.35524453 1.93340273 -0.66480758 -0.13402365 -0.5497420 -0.65437128 -0.2106793 0.50833502
gs16 -0.49794597 0.11173796 -0.25559084 0.22339202 -0.64200232 -1.06027171 -0.2890369 1.19556001 -0.4032416 1.25356657 0.17652910 -0.19476214 1.266689482 -0.1247642 -0.559948207 -0.01704689 -0.72464431 -2.20081384 -0.15376113 -1.85192168 -0.07973415 -1.16618073 0.91452163 -1.01623802 -0.53633071 0.65478475 1.3545217 1.67222330 1.3510851 1.59962370
gs17 -0.09192484 -0.81489259 0.44113992 1.50083666 0.02989752 -0.07702809 1.1216086 -0.58155914 -1.0886995 -0.73736123 -0.32942151 -0.04370937 0.314676528 0.9820022 -0.208601981 -1.16796258 -0.67938471 -2.70665603 -0.77318960 1.15353807 2.12147238 0.58452002 0.02454425 1.82856706 1.65015182 -1.15785073 0.3546658 -0.34445966 -1.0254307 -0.27948863
gs18 -0.31852173 0.12067183 -1.25950009 0.76892943 0.46096286 -0.26662836 0.4417647 0.79129254 -1.9726560 0.43035752 0.45698355 -0.29005193 -1.813833043 0.3629808 0.236509319 -1.42021611 -1.05453320 1.41161896 1.36173027 0.77494149 0.84023752 0.38901914 0.95885634 -0.50800307 -0.67393504 -0.48992210 0.7004933 1.31021998 -0.6332057 -1.11656327
gs19 0.72641579 -0.57769847 0.49329687 -0.51183227 -1.11400559 0.64877026 -0.4406262 0.25071309 2.1136039 -0.52679579 -2.43932744 0.77103343 0.910888191 -0.9678455 -0.009019031 -0.62004911 0.32332812 1.08838097 -0.12574913 -1.57352212 -0.59724213 1.14917069 0.80924032 0.92711227 1.00116247 -0.06280573 1.2499995 -0.85619615 -1.1394307 -0.90097052
gs20 -0.40686085 -0.19758125 -0.45781926 -0.55886885 -0.12951342 -0.54918118 -1.4879999 0.82768742 1.1492282 0.52844266 0.52775384 -0.40217918 1.624947601 0.2093448 -0.333895058 0.11284783 2.10468712 -1.29927604 -1.42891137 -0.32736265 1.53004416 0.70793130 0.01872158 1.27121937 -0.41694874 -1.75501137 0.7076323 0.34166052 -2.2272134 0.31647390
gs21 0.11064959 0.63071460 -0.09315791 0.73101162 -1.00749109 -0.53271009 0.2591944 1.13172316 0.1506891 -0.87646695 -1.69439296 0.83702971 1.876937011 1.4478442 0.482520953 -1.29624843 0.76274193 0.01335892 0.67731457 -1.29116635 0.12279982 -0.42496995 -0.69988173 0.61045071 1.12362505 -0.26701006 -0.9392599 -0.83744301 0.2756659 -1.28407286
gs22 1.69743076 -0.62568897 0.95318018 0.79835944 -0.22877959 -0.33245259 -0.8818449 -0.07048306 0.3842529 0.59890023 1.19876650 0.89702407 -0.063815196 0.1767625 -0.247788166 -0.12757217 -0.78058894 -1.35990624 0.57884316 -0.32914348 -1.97746404 -0.96013904 -2.12070233 -0.60051457 0.51066179 0.92360209 1.2892500 -0.50402715 0.2956685 0.90820836
gs23 0.60506926 0.44111596 -1.65790604 -1.19005302 -1.63334726 1.91345338 0.1927653 -0.63878889 0.5837665 1.18492028 -0.46232575 -1.20423315 -0.218426414 -0.3260477 0.028282249 -0.12215401 -0.65082403 -0.57846899 0.78152042 0.48778655 0.95493242 -0.81023527 -0.15048463 1.44187787 0.77550222 0.23753821 -1.3126729 1.58523096 -0.4605529 0.20275941
gs24 -0.72148839 -0.54576956 -1.18688036 0.89207321 1.69203360 1.73911075 0.9927791 0.68541378 -0.1858115 -0.67635067 -0.95993033 -1.11607732 0.647530634 -0.7736508 -0.323911174 0.09530263 -0.01217018 0.24474840 1.24467781 0.01803482 -0.25900876 0.65090463 -1.30503212 -2.43406616 0.67009734 0.97148066 0.2259098 -0.36238688 1.8322860 -1.73984886
gs25 0.18453756 -1.41154192 1.23729871 0.79812134 0.08096990 -0.28095732 0.5439363 0.76789568 -0.5449132 1.23698241 0.43459496 -0.96638207 -1.685807242 0.3305633 -0.725234936 -0.20714446 -0.66613185 -0.41593820 -1.07617312 -0.64173119 0.11884874 2.77574824 0.54647524 -0.11517645 0.01675019 -0.66013610 0.1421437 -0.20674328 1.0131497 -0.62400460
>
> stopifnot(identical(featureNames(huangArrayRMAnoBatchCommon_eset),
+ featureNames(pickrellCountsArgonneCQNcommon_eset)))
> stopifnot(identical(sampleNames(huangArrayRMAnoBatchCommon_eset),
+ sampleNames(pickrellCountsArgonneCQNcommon_eset)))
> ## until the updated GSVAdata goes through the build system
> ## remove duplicated rows
> fnames <- featureNames(huangArrayRMAnoBatchCommon_eset)
> mask <- duplicated(fnames)
> huangArrayRMAnoBatchCommon_eset <- huangArrayRMAnoBatchCommon_eset[!mask, ]
> pickrellCountsArgonneCQNcommon_eset <- pickrellCountsArgonneCQNcommon_eset[!mask, ]
>
> 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)
> 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)
> 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)
> 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 | 0.032 | 0.001 | 0.033 | |
| filterGeneSets | 0 | 0 | 0 | |
| gsva | 0.210 | 0.044 | 0.254 | |
| gsvaEnrichment | 0.052 | 0.016 | 0.069 | |
| gsvaParam-class | 0.962 | 0.089 | 1.075 | |
| gsvaRanks | 0.125 | 0.000 | 0.126 | |
| igsva | 0 | 0 | 0 | |
| plageParam-class | 0.706 | 0.017 | 0.722 | |
| readGMT | 10.424 | 0.363 | 10.791 | |
| ssgseaParam-class | 0.737 | 0.010 | 0.747 | |
| zscoreParam-class | 0.822 | 0.018 | 0.840 | |