Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 136/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BASiCS 2.18.0 (landing page) Catalina Vallejos
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the BASiCS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BASiCS.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: BASiCS |
Version: 2.18.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BASiCS_2.18.0.tar.gz |
StartedAt: 2024-12-19 23:57:48 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-20 00:16:59 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 1151.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BASiCS.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BASiCS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BASiCS_2.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BASiCS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BASiCS’ version ‘2.18.0’ * 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 ‘BASiCS’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... 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 BASiCS_TestDE 15.236 0.115 15.584 BASiCS_MCMC 11.770 0.167 12.570 BASiCS_PlotDE 7.887 0.048 8.493 newBASiCS_Chain 5.432 0.065 5.557 BASiCS_Chain 5.259 0.162 5.944 BASiCS_VarThresholdSearchHVG_LVG 4.762 0.227 5.041 BASiCS_DiagPlot 4.840 0.026 5.304 BASiCS_DivideAndConquer 3.717 0.069 56.170 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/00check.log’ for details.
BASiCS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BASiCS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘BASiCS’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c BASiCS.cpp -o BASiCS.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BASiCS.so BASiCS.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-BASiCS/00new/BASiCS/libs ** R ** data ** 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 (BASiCS)
BASiCS.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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. > library(testthat) > library(BASiCS) Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Welcome to 'BASiCS'. If you used 'BASiCS' before its release in Bioconductor, please visit: https://github.com/catavallejos/BASiCS/wiki. > > test_check("BASiCS") ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6714 (ratio SC vs P&S). ------------------------------------------------------------- ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6714 (ratio SC vs P&S). To visualise its effect, please use 'PlotOffset = TRUE'. ------------------------------------------------------------- ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6714 (ratio Group1 vs Group2). To visualise its effect, please use 'PlotOffset = TRUE'. ------------------------------------------------------------- For Differential mean task: the posterior probability threshold chosen via EFDR calibration is too low. Probability threshold automatically set equal to 'ProbThresholdM'. EFDR calibration failed for Differential dispersion task. Probability threshold automatically set equal to 'ProbThresholdD'. ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6714 (ratio SC vs P&S). To visualise its effect, please use 'PlotOffset = TRUE'. ------------------------------------------------------------- ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6714 (ratio Group1 vs Group2). ------------------------------------------------------------- For Differential mean task: the posterior probability threshold chosen via EFDR calibration is too low. Probability threshold automatically set equal to 'ProbThresholdM'. EFDR calibration failed for Differential dispersion task. Probability threshold automatically set equal to 'ProbThresholdD'. ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6714 (ratio SC vs P&S). To visualise its effect, please use 'PlotOffset = TRUE'. ------------------------------------------------------------- ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6714 (ratio SC vs P&S). To visualise its effect, please use 'PlotOffset = TRUE'. ------------------------------------------------------------- ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6787 (ratio SC vs P&S). To visualise its effect, please use 'PlotOffset = TRUE'. ------------------------------------------------------------- ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6787 (ratio Group1 vs Group2). To visualise its effect, please use 'PlotOffset = TRUE'. ------------------------------------------------------------- ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6787 (ratio Group1 vs Group2). To visualise its effect, please use 'PlotOffset = TRUE'. ------------------------------------------------------------- EFDR calibration failed for Differential mean task. Probability threshold automatically set equal to 'ProbThresholdM'. EFDR calibration failed for Differential dispersion task. Probability threshold automatically set equal to 'ProbThresholdD'. For Differential residual dispersion task: the posterior probability threshold chosen via EFDR calibration is too low. Probability threshold automatically set equal to 'ProbThresholdR'. ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6787 (ratio SC vs P&S). To visualise its effect, please use 'PlotOffset = TRUE'. ------------------------------------------------------------- ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6787 (ratio Group1 vs Group2). To visualise its effect, please use 'PlotOffset = TRUE'. ------------------------------------------------------------- EFDR calibration failed for Differential mean task. Probability threshold automatically set equal to 'ProbThresholdM'. EFDR calibration failed for Differential dispersion task. Probability threshold automatically set equal to 'ProbThresholdD'. For Differential residual dispersion task: the posterior probability threshold chosen via EFDR calibration is too low. Probability threshold automatically set equal to 'ProbThresholdR'. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.016 system: 0 elapsed: 0.017 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.018 system: 0.001 elapsed: 0.018 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.016 system: 0 elapsed: 0.017 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.018 system: 0 elapsed: 0.018 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- Combining batch posteriors for mu Combining batch posteriors for delta Combining batch posteriors for phi Combining batch posteriors for s Combining batch posteriors for nu Combining batch posteriors for theta Combining batch posteriors for beta Combining batch posteriors for sigma2 Combining batch posteriors for epsilon Combining batch posteriors for RBFLocations altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.014 system: 0 elapsed: 0.015 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.016 system: 0 elapsed: 0.016 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- Combining batch posteriors for mu Combining batch posteriors for delta Combining batch posteriors for phi Combining batch posteriors for s Combining batch posteriors for nu Combining batch posteriors for theta Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.015 system: 0 elapsed: 0.014 ------------------------------------------------------------- Output ------------------------------------------------------------- Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.017 system: 0.001 elapsed: 0.017 ------------------------------------------------------------- Output ------------------------------------------------------------- Combining batch posteriors for mu Combining batch posteriors for delta Combining batch posteriors for s Combining batch posteriors for nu Combining batch posteriors for theta Combining batch posteriors for beta Combining batch posteriors for sigma2 Combining batch posteriors for epsilon Combining batch posteriors for RBFLocations ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.012 system: 0 elapsed: 0.014 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.015 system: 0 elapsed: 0.016 ------------------------------------------------------------- Output ------------------------------------------------------------- Combining batch posteriors for mu Combining batch posteriors for delta Combining batch posteriors for s Combining batch posteriors for nu Combining batch posteriors for theta altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.018 system: 0 elapsed: 0.02 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.016 system: 0 elapsed: 0.018 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- Combining batch posteriors for mu Combining batch posteriors for delta Combining batch posteriors for phi Combining batch posteriors for s Combining batch posteriors for nu Combining batch posteriors for theta Combining batch posteriors for beta Combining batch posteriors for sigma2 Combining batch posteriors for epsilon Combining batch posteriors for RBFLocations altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.013 system: 0 elapsed: 0.014 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.016 system: 0 elapsed: 0.016 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- Combining batch posteriors for mu Combining batch posteriors for delta Combining batch posteriors for phi Combining batch posteriors for s Combining batch posteriors for nu Combining batch posteriors for theta Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.016 system: 0.001 elapsed: 0.019 ------------------------------------------------------------- Output ------------------------------------------------------------- Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.015 system: 0 elapsed: 0.015 ------------------------------------------------------------- Output ------------------------------------------------------------- Combining batch posteriors for mu Combining batch posteriors for delta Combining batch posteriors for s Combining batch posteriors for nu Combining batch posteriors for theta Combining batch posteriors for beta Combining batch posteriors for sigma2 Combining batch posteriors for epsilon Combining batch posteriors for RBFLocations ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.011 system: 0 elapsed: 0.016 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.014 system: 0 elapsed: 0.023 ------------------------------------------------------------- Output ------------------------------------------------------------- Combining batch posteriors for mu Combining batch posteriors for delta Combining batch posteriors for s Combining batch posteriors for nu Combining batch posteriors for theta ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.024 system: 0 elapsed: 0.026 ------------------------------------------------------------- Output ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.105 system: 0.001 elapsed: 0.113 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.11 system: 0 elapsed: 0.121 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- Combining batch posteriors for mu Combining batch posteriors for delta Combining batch posteriors for phi Combining batch posteriors for s Combining batch posteriors for nu Combining batch posteriors for theta Combining batch posteriors for beta Combining batch posteriors for sigma2 Combining batch posteriors for epsilon Combining batch posteriors for RBFLocations Combining batch posteriors for mu Combining batch posteriors for delta Combining batch posteriors for phi Combining batch posteriors for s Combining batch posteriors for nu Combining batch posteriors for theta Combining batch posteriors for beta Combining batch posteriors for sigma2 Combining batch posteriors for epsilon Combining batch posteriors for RBFLocations Combining batch posteriors for mu Combining batch posteriors for mu Combining batch posteriors for delta Combining batch posteriors for phi Combining batch posteriors for s Combining batch posteriors for nu Combining batch posteriors for theta Cannot find a balanced split with 9 quantiles, trying again with 8 altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.115 system: 0.001 elapsed: 0.122 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.104 system: 0 elapsed: 0.104 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- Generating partitions... Starting MCMC... ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ----------------------------------------------------- MCMC sampler has been started: 200 iterations to go. ----------------------------------------------------- RefGene: 0 RefGene: 44 RefGene: 0 RefGene: 16 RefGene: 16 RefGene: 39 RefGene: 16 RefGene: 17 RefGene: 11 RefGene: 31 RefGene: 16 RefGene: 31 RefGene: 17 RefGene: 11 RefGene: 39 RefGene: 43 RefGene: 44 RefGene: 16 RefGene: 13 RefGene: 13 RefGene: 31 RefGene: 39 RefGene: 11 RefGene: 16 RefGene: 11 RefGene: 13 RefGene: 11 RefGene: 43 RefGene: 44 RefGene: 13 RefGene: 44 RefGene: 13 RefGene: 11 RefGene: 39 RefGene: 39 RefGene: 13 RefGene: 43 RefGene: 0 RefGene: 39 RefGene: 16 RefGene: 11 RefGene: 31 RefGene: 15 RefGene: 44 RefGene: 13 RefGene: 15 RefGene: 15 RefGene: 44 RefGene: 0 RefGene: 39 RefGene: 16 RefGene: 17 RefGene: 31 RefGene: 39 RefGene: 13 RefGene: 13 RefGene: 0 RefGene: 17 RefGene: 31 RefGene: 0 RefGene: 16 RefGene: 39 RefGene: 16 RefGene: 17 RefGene: 16 RefGene: 44 RefGene: 16 RefGene: 16 RefGene: 0 RefGene: 11 RefGene: 39 RefGene: 0 RefGene: 17 RefGene: 15 RefGene: 43 RefGene: 13 RefGene: 15 RefGene: 13 RefGene: 15 RefGene: 43 RefGene: 39 RefGene: 43 RefGene: 15 RefGene: 43 RefGene: 13 RefGene: 43 RefGene: 16 RefGene: 17 RefGene: 15 RefGene: 11 RefGene: 39 RefGene: 43 RefGene: 31 RefGene: 15 RefGene: 31 RefGene: 43 RefGene: 44 RefGene: 16 RefGene: 16 RefGene: 31 ----------------------------------------------------- End of Burn-in period. ----------------------------------------------------- RefGene: 39 RefGene: 31 RefGene: 43 RefGene: 15 RefGene: 11 RefGene: 44 RefGene: 31 RefGene: 17 RefGene: 0 RefGene: 31 RefGene: 17 RefGene: 16 RefGene: 11 RefGene: 15 RefGene: 11 RefGene: 39 RefGene: 0 RefGene: 15 RefGene: 43 RefGene: 44 RefGene: 31 RefGene: 31 RefGene: 31 RefGene: 15 RefGene: 16 RefGene: 17 RefGene: 43 RefGene: 13 RefGene: 17 RefGene: 13 RefGene: 13 RefGene: 39 RefGene: 43 RefGene: 15 RefGene: 15 RefGene: 13 RefGene: 39 RefGene: 44 RefGene: 39 RefGene: 17 RefGene: 31 RefGene: 39 RefGene: 16 RefGene: 39 RefGene: 39 RefGene: 11 RefGene: 13 RefGene: 43 RefGene: 31 RefGene: 15 RefGene: 11 RefGene: 43 RefGene: 17 RefGene: 15 RefGene: 39 RefGene: 44 RefGene: 44 RefGene: 16 RefGene: 11 RefGene: 11 RefGene: 0 RefGene: 11 RefGene: 13 RefGene: 15 RefGene: 16 RefGene: 39 RefGene: 15 RefGene: 17 RefGene: 0 RefGene: 11 RefGene: 31 RefGene: 31 RefGene: 43 RefGene: 16 RefGene: 31 RefGene: 0 RefGene: 15 RefGene: 43 RefGene: 15 RefGene: 43 RefGene: 43 RefGene: 17 RefGene: 11 RefGene: 13 RefGene: 31 RefGene: 43 RefGene: 13 RefGene: 31 RefGene: 44 RefGene: 44 RefGene: 11 RefGene: 39 RefGene: 16 RefGene: 31 RefGene: 31 RefGene: 11 RefGene: 43 RefGene: 11 RefGene: 17 RefGene: 13 ----------------------------------------------------- ----------------------------------------------------- All 200 MCMC iterations have been completed. ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- Please see below a summary of the overall acceptance rates. ----------------------------------------------------- Minimum acceptance rate among mu[i]'s: 0.14 Average acceptance rate among mu[i]'s: 0.5016 Maximum acceptance rate among mu[i]'s: 0.75 Minimum acceptance rate among delta[i]'s: 0.51 Average acceptance rate among delta[i]'s: 0.6786 Maximum acceptance rate among delta[i]'s: 0.81 Minimum acceptance rate among nu[jk]'s: 0.8 Average acceptance rate among nu[jk]'s: 0.9452 Maximum acceptance rate among nu[jk]'s: 1 Minimum acceptance rate among theta[k]'s: 1 Average acceptance rate among theta[k]'s: 1 Maximum acceptance rate among theta[k]'s: 1 ----------------------------------------------------- ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.31 system: 0.003 elapsed: 0.382 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ----------------------------------------------------- MCMC sampler has been started: 200 iterations to go. ----------------------------------------------------- RefGene: 23 RefGene: 22 RefGene: 19 RefGene: 14 RefGene: 36 RefGene: 22 RefGene: 49 RefGene: 10 RefGene: 23 RefGene: 9 RefGene: 23 RefGene: 11 RefGene: 19 RefGene: 19 RefGene: 49 RefGene: 49 RefGene: 11 RefGene: 36 RefGene: 49 RefGene: 10 RefGene: 47 RefGene: 10 RefGene: 23 RefGene: 10 RefGene: 36 RefGene: 11 RefGene: 9 RefGene: 14 RefGene: 14 RefGene: 19 RefGene: 9 RefGene: 11 RefGene: 10 RefGene: 14 RefGene: 47 RefGene: 14 RefGene: 9 RefGene: 23 RefGene: 10 RefGene: 14 RefGene: 10 RefGene: 10 RefGene: 49 RefGene: 19 RefGene: 36 RefGene: 49 RefGene: 11 RefGene: 14 RefGene: 49 RefGene: 49 RefGene: 36 RefGene: 11 RefGene: 22 RefGene: 11 RefGene: 47 RefGene: 19 RefGene: 14 RefGene: 10 RefGene: 23 RefGene: 19 RefGene: 11 RefGene: 22 RefGene: 23 RefGene: 19 RefGene: 23 RefGene: 23 RefGene: 19 RefGene: 9 RefGene: 23 RefGene: 49 RefGene: 19 RefGene: 14 RefGene: 11 RefGene: 23 RefGene: 36 RefGene: 10 RefGene: 9 RefGene: 9 RefGene: 10 RefGene: 19 RefGene: 11 RefGene: 11 RefGene: 9 RefGene: 10 RefGene: 11 RefGene: 14 RefGene: 9 RefGene: 22 RefGene: 14 RefGene: 36 RefGene: 22 RefGene: 49 RefGene: 22 RefGene: 49 RefGene: 14 RefGene: 36 RefGene: 19 RefGene: 47 RefGene: 22 RefGene: 14 ----------------------------------------------------- End of Burn-in period. ----------------------------------------------------- RefGene: 14 RefGene: 47 RefGene: 47 RefGene: 47 RefGene: 23 RefGene: 9 RefGene: 49 RefGene: 11 RefGene: 47 RefGene: 49 RefGene: 14 RefGene: 23 RefGene: 10 RefGene: 19 RefGene: 47 RefGene: 14 RefGene: 22 RefGene: 36 RefGene: 19 RefGene: 36 RefGene: 14 RefGene: 19 RefGene: 22 RefGene: 9 RefGene: 49 RefGene: 14 RefGene: 23 RefGene: 49 RefGene: 14 RefGene: 9 RefGene: 36 RefGene: 22 RefGene: 19 RefGene: 23 RefGene: 9 RefGene: 14 RefGene: 14 RefGene: 10 RefGene: 36 RefGene: 47 RefGene: 19 RefGene: 9 RefGene: 47 RefGene: 10 RefGene: 10 RefGene: 22 RefGene: 10 RefGene: 36 RefGene: 19 RefGene: 11 RefGene: 9 RefGene: 47 RefGene: 47 RefGene: 9 RefGene: 23 RefGene: 9 RefGene: 36 RefGene: 22 RefGene: 36 RefGene: 22 RefGene: 47 RefGene: 22 RefGene: 10 RefGene: 9 RefGene: 22 RefGene: 14 RefGene: 36 RefGene: 47 RefGene: 36 RefGene: 9 RefGene: 11 RefGene: 9 RefGene: 10 RefGene: 36 RefGene: 10 RefGene: 23 RefGene: 23 RefGene: 10 RefGene: 9 RefGene: 36 RefGene: 49 RefGene: 10 RefGene: 9 RefGene: 49 RefGene: 14 RefGene: 47 RefGene: 23 RefGene: 22 RefGene: 9 RefGene: 9 RefGene: 47 RefGene: 9 RefGene: 11 RefGene: 23 RefGene: 11 RefGene: 19 RefGene: 9 RefGene: 9 RefGene: 11 RefGene: 9 ----------------------------------------------------- ----------------------------------------------------- All 200 MCMC iterations have been completed. ----------------------------------------------------- ----------------------------------------------------- ----------------------------------------------------- Please see below a summary of the overall acceptance rates. ----------------------------------------------------- Minimum acceptance rate among mu[i]'s: 0.18 Average acceptance rate among mu[i]'s: 0.5074 Maximum acceptance rate among mu[i]'s: 0.76 Minimum acceptance rate among delta[i]'s: 0.58 Average acceptance rate among delta[i]'s: 0.6892 Maximum acceptance rate among delta[i]'s: 0.79 Minimum acceptance rate among nu[jk]'s: 0.83 Average acceptance rate among nu[jk]'s: 0.9554 Maximum acceptance rate among nu[jk]'s: 1 Minimum acceptance rate among theta[k]'s: 1 Average acceptance rate among theta[k]'s: 1 Maximum acceptance rate among theta[k]'s: 1 ----------------------------------------------------- ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.299 system: 0.001 elapsed: 0.317 ------------------------------------------------------------- Output ------------------------------------------------------------- Combining batch posteriors for mu Combining batch posteriors for delta Combining batch posteriors for s Combining batch posteriors for nu Combining batch posteriors for theta sumAux (line 117): 146.424 sumAux (line 117): 136.459 For LVG detection task: the posterior probability threshold chosen via EFDR calibration is too low. Probability threshold automatically set equal to 'ProbThreshold'. For LVG detection task: the posterior probability threshold chosen via EFDR calibration is too low. Probability threshold automatically set equal to 'ProbThreshold'. For LVG detection task: the posterior probability threshold chosen via EFDR calibration is too low. Probability threshold automatically set equal to 'ProbThreshold'. Evaluating variance contribution threshold = 25 % ... Evaluating variance contribution threshold = 50 % ... Evaluating variance contribution threshold = 75 % ... Evaluating variance contribution threshold = 25 % ... Evaluating variance contribution threshold = 50 % ... Evaluating variance contribution threshold = 75 % ... For LVG detection task: the posterior probability threshold chosen via EFDR calibration is too low. Probability threshold automatically set equal to 'ProbThreshold'. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.008 system: 0 elapsed: 0.008 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.009 system: 0 elapsed: 0.009 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.016 system: 0 elapsed: 0.017 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.006 system: 0 elapsed: 0.007 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.007 system: 0 elapsed: 0.006 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.011 system: 0 elapsed: 0.013 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.011 system: 0 elapsed: 0.012 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.006 system: 0 elapsed: 0.007 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.006 system: 0 elapsed: 0.006 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.006 system: 0 elapsed: 0.008 ------------------------------------------------------------- Output ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.008 system: 0 elapsed: 0.009 ------------------------------------------------------------- Output ------------------------------------------------------------- Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.008 system: 0 elapsed: 0.009 ------------------------------------------------------------- Output ------------------------------------------------------------- Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.008 system: 0 elapsed: 0.009 ------------------------------------------------------------- Output ------------------------------------------------------------- Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.008 system: 0 elapsed: 0.008 ------------------------------------------------------------- Output ------------------------------------------------------------- Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.009 system: 0 elapsed: 0.008 ------------------------------------------------------------- Output ------------------------------------------------------------- Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.008 system: 0 elapsed: 0.01 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.011 system: 0 elapsed: 0.011 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.011 system: 0 elapsed: 0.011 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.011 system: 0 elapsed: 0.011 ------------------------------------------------------------- Output ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.007 system: 0 elapsed: 0.007 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.008 system: 0 elapsed: 0.009 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.009 system: 0 elapsed: 0.009 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.012 system: 0 elapsed: 0.014 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS_Chain object stored as chain_.Rds file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- ------------------------------------------------------------- Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.016 system: 0 elapsed: 0.016 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS_Chain object stored as chain_.Rds file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- ------------------------------------------------------------- Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.012 system: 0 elapsed: 0.012 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS_Chain object stored as chain_.Rds file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- ------------------------------------------------------------- Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : horizontal integration (no-spikes case) ------------------------------------------------------------- Randomly, 1 out of 10 genes was left as reference at each iteration List of reference genes and frequencies stored as a .txt file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.015 system: 0 elapsed: 0.016 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS_Chain object stored as chain_.Rds file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- ------------------------------------------------------------- Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : horizontal integration (no-spikes case) ------------------------------------------------------------- Randomly, 1 out of 10 genes was left as reference at each iteration List of reference genes and frequencies stored as a .txt file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.012 system: 0 elapsed: 0.013 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- `BASiCS_Chain` class definition was outdated. Object updated to be compatible with BASiCS version 2.18.0. Set 'StoreUpdatedChain' = TRUE to save updated object. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.012 system: 0 elapsed: 0.013 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- `BASiCS_Chain` class definition was outdated. Object updated to be compatible with BASiCS version 2.18.0. Set 'StoreUpdatedChain' = TRUE to save updated object. (this overwrites original input file). ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 1 (ratio Group1 vs Group2). ------------------------------------------------------------- EFDR calibration failed for Differential mean task. Probability threshold automatically set equal to 'ProbThresholdM'. EFDR calibration failed for Differential dispersion task. Probability threshold automatically set equal to 'ProbThresholdD'. EFDR calibration failed for Differential residual dispersion task. Probability threshold automatically set equal to 'ProbThresholdR'. Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.036 system: 0 elapsed: 0.036 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 1 (ratio Group1 vs Group2). ------------------------------------------------------------- EFDR calibration failed for Differential mean task. Probability threshold automatically set equal to 'ProbThresholdM'. EFDR calibration failed for Differential dispersion task. Probability threshold automatically set equal to 'ProbThresholdD'. EFDR calibration failed for Differential residual dispersion task. Probability threshold automatically set equal to 'ProbThresholdR'. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.576 system: 0.002 elapsed: 0.607 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.005 system: 0.001 elapsed: 0.006 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.576 system: 0.003 elapsed: 0.614 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.535 system: 0.004 elapsed: 0.561 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.536 system: 0.002 elapsed: 0.566 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.005 system: 0 elapsed: 0.005 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.513 system: 0.002 elapsed: 0.53 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.509 system: 0.002 elapsed: 0.544 ------------------------------------------------------------- Output ------------------------------------------------------------- Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.984 system: 0.014 elapsed: 1.067 ------------------------------------------------------------- Output ------------------------------------------------------------- Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.983 system: 0.008 elapsed: 1.049 ------------------------------------------------------------- Output ------------------------------------------------------------- Running no spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.037 system: 0 elapsed: 0.037 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.746 system: 0.002 elapsed: 0.786 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.007 system: 0 elapsed: 0.007 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- Storing trajectories of adaptive proposal variances (log-scale) aschain_ls_.Rds file in '/Users/biocbuild/bbs-3.20-bioc/meat/BASiCS.Rcheck/tests/testthat' directory ... ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6714 (ratio Group1 vs Group2). To visualise its effect, please use 'PlotOffset = TRUE'. ------------------------------------------------------------- For Differential mean task: the posterior probability threshold chosen via EFDR calibration is too low. Probability threshold automatically set equal to 'ProbThresholdM'. EFDR calibration failed for Differential dispersion task. Probability threshold automatically set equal to 'ProbThresholdD'. ------------------------------------------------------------- Log-fold change thresholds are now set in a log2 scale. Original BASiCS release used a natural logarithm scale. ------------------------------------------------------------- Offset estimate: 0.6787 (ratio Group1 vs Group2). To visualise its effect, please use 'PlotOffset = TRUE'. ------------------------------------------------------------- EFDR calibration failed for Differential mean task. Probability threshold automatically set equal to 'ProbThresholdM'. EFDR calibration failed for Differential dispersion task. Probability threshold automatically set equal to 'ProbThresholdD'. For Differential residual dispersion task: the posterior probability threshold chosen via EFDR calibration is too low. Probability threshold automatically set equal to 'ProbThresholdR'. altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.008 system: 0.001 elapsed: 0.008 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.009 system: 0 elapsed: 0.011 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.008 system: 0 elapsed: 0.008 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. Running with spikes BASiCS sampler (regression case) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.008 system: 0 elapsed: 0.008 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. 'BatchInfo' was treated as a factor with 2 levels: 1 2 'BatchInfo' was treated as a factor with 2 levels: 1 2 ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running no spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.006 system: 0 elapsed: 0.005 ------------------------------------------------------------- Output ------------------------------------------------------------- 'BatchInfo' was treated as a factor with 2 levels: 1 2 altExp 'spike-ins' is assumed to contain spike-in genes. see help(altExp) for details. ------------------------------------------------------------- NOTE: default choice PriorDelta = 'log-normal' (recommended value). Vallejos et al (2015) used a 'gamma' prior instead. ------------------------------------------------------------- Running with spikes BASiCS sampler (no regression) ... ------------------------------------------------------------- MCMC running time ------------------------------------------------------------- user: 0.007 system: 0 elapsed: 0.007 ------------------------------------------------------------- Output ------------------------------------------------------------- ------------------------------------------------------------- BASiCS version 2.18.0 : vertical integration (spikes case) ------------------------------------------------------------- [ FAIL 0 | WARN 0 | SKIP 0 | PASS 459 ] > > proc.time() user system elapsed 375.683 6.356 494.579
BASiCS.Rcheck/BASiCS-Ex.timings
name | user | system | elapsed | |
BASiCS_Chain-methods | 3.982 | 0.085 | 4.440 | |
BASiCS_Chain | 5.259 | 0.162 | 5.944 | |
BASiCS_CorrectOffset | 0.022 | 0.009 | 0.034 | |
BASiCS_DenoisedCounts | 3.259 | 0.044 | 3.622 | |
BASiCS_DenoisedRates | 3.119 | 0.030 | 3.476 | |
BASiCS_DetectVG | 1.816 | 0.105 | 2.114 | |
BASiCS_DiagHist | 2.374 | 0.052 | 2.639 | |
BASiCS_DiagPlot | 4.840 | 0.026 | 5.304 | |
BASiCS_DivideAndConquer | 3.717 | 0.069 | 56.170 | |
BASiCS_Draw | 0.471 | 0.013 | 0.498 | |
BASiCS_EffectiveSize | 0.482 | 0.018 | 0.522 | |
BASiCS_Filter | 0.004 | 0.001 | 0.005 | |
BASiCS_LoadChain | 2.640 | 0.027 | 2.788 | |
BASiCS_MCMC | 11.770 | 0.167 | 12.570 | |
BASiCS_MockSCE | 0.482 | 0.005 | 0.508 | |
BASiCS_PlotDE | 7.887 | 0.048 | 8.493 | |
BASiCS_PlotOffset | 2.283 | 0.022 | 2.475 | |
BASiCS_PlotVG | 0.756 | 0.016 | 0.810 | |
BASiCS_PriorParam | 0.385 | 0.009 | 0.429 | |
BASiCS_ShowFit | 0.565 | 0.009 | 0.625 | |
BASiCS_Sim | 1.018 | 0.013 | 1.128 | |
BASiCS_Summary-methods | 0.007 | 0.004 | 0.011 | |
BASiCS_Summary | 2.851 | 0.039 | 3.029 | |
BASiCS_TestDE | 15.236 | 0.115 | 15.584 | |
BASiCS_VarThresholdSearchHVG_LVG | 4.762 | 0.227 | 5.041 | |
BASiCS_VarianceDecomp | 0.431 | 0.009 | 0.443 | |
Summary-BASiCS_Chain-method | 0.457 | 0.006 | 0.466 | |
dim-BASiCS_Chain-method | 0.009 | 0.013 | 0.022 | |
dimnames-BASiCS_Chain-method | 0.010 | 0.015 | 0.025 | |
displayChainBASiCS-BASiCS_Chain-method | 0.267 | 0.078 | 0.382 | |
displaySummaryBASiCS-BASiCS_Summary-method | 0.248 | 0.054 | 0.310 | |
makeExampleBASiCS_Data | 0.384 | 0.005 | 0.426 | |
newBASiCS_Chain | 5.432 | 0.065 | 5.557 | |
plot-BASiCS_Chain-method | 0.227 | 0.050 | 0.281 | |
plot-BASiCS_Summary-method | 0.233 | 0.053 | 0.290 | |
show-BASiCS_ResultDE-method | 0.236 | 0.050 | 0.290 | |
show-BASiCS_ResultVG-method | 0.236 | 0.052 | 0.294 | |
show-BASiCS_ResultsDE-method | 0.235 | 0.055 | 0.295 | |
subset-BASiCS_Chain-method | 1.990 | 0.013 | 2.006 | |