about running gsva on mac

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Ed ▴ 230

@ed-4683

Last seen 9.6 years ago

Hi there, I used the examples in ?gsva and got the following errors on my mac. However, I run it also on the linux and it worked. Please suggest. Thanks, Weiwei > library(limma) > > p <- 10 ## number of genes > n <- 30 ## number of samples > nGrp1 <- 15 ## number of samples in group 1 > nGrp2 <- n - nGrp1 ## number of samples in group 2 > > ## consider three disjoint gene sets > geneSets <- list(set1=paste("g", 1:3, sep=""), + set2=paste("g", 4:6, sep=""), + set3=paste("g", 7:10, sep="")) > > ## sample data from a normal distribution with mean 0 and st.dev. 1 > y <- matrix(rnorm(n*p), nrow=p, ncol=n, + dimnames=list(paste("g", 1:p, sep="") , paste("s", 1:n, sep=""))) > > ## genes in set1 are expressed at higher levels in the last 10 samples > y[geneSets$set1, (nGrp1+1):n] <- y[geneSets$set1, (nGrp1+1):n] + 2 > > ## build design matrix > design <- cbind(sampleGroup1=1, sampleGroup2vs1=c(rep(0, nGrp1), rep(1, nGrp2))) > > ## fit linear model > fit <- lmFit(y, design) > > ## estimate moderated t-statistics > fit <- eBayes(fit) > > ## genes in set1 are differentially expressed > topTable(fit, coef="sampleGroup2vs1") ID logFC t P.Value adj.P.Val B 2 g2 2.43865785 6.79741169 1.490585e-09 1.490585e-08 11.467181 1 g1 1.81349993 5.04733755 2.590932e-06 1.295466e-05 4.218446 3 g3 1.68971708 4.54930258 1.812937e-05 6.043122e-05 2.348424 5 g5 0.25263973 0.65201092 5.161890e-01 9.308575e-01 -6.688660 10 g10 0.16766254 0.49082930 6.248376e-01 9.308575e-01 -6.780571 9 g9 0.13478444 0.40143265 6.891295e-01 9.308575e-01 -6.820434 8 g8 -0.12067327 -0.32614302 7.451340e-01 9.308575e-01 -6.847833 7 g7 -0.08002351 -0.23401984 8.155437e-01 9.308575e-01 -6.873660 4 g4 0.07875803 0.20538583 8.377717e-01 9.308575e-01 -6.879960 6 g6 -0.03196719 -0.08251146 9.344379e-01 9.344379e-01 -6.897676 > > ## estimate GSVA enrichment scores for the three sets > gsva_es <- gsva(y, geneSets, mx.diff=1)$es.obs | | 0%The process has forked and you cannot use this CoreFoundation functionality safely. You MUST exec(). Break on __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNCTI ONALITY___YOU_MUST_EXEC__() to debug. The process has forked and you can > version _ platform x86_64-apple-darwin10.8.0 arch x86_64 os darwin10.8.0 system x86_64, darwin10.8.0 status major 3 minor 0.1 year 2013 month 05 day 16 svn rev 62743 language R version.string R version 3.0.1 (2013-05-16) nickname Good Sport > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.16.7 GSVA_1.8.0 GSEABase_1.22.0 graph_1.38.3 [5] annotate_1.38.0 AnnotationDbi_1.22.6 Biobase_2.20.1 BiocGenerics_0.6.0 [9] BiocInstaller_1.10.3 loaded via a namespace (and not attached): [1] DBI_0.2-7 grid_3.0.1 IRanges_1.18.2 lattice_0.20-15 Matrix_1.0-12 [6] RSQLite_0.11.4 stats4_3.0.1 tools_3.0.1 XML_3.95-0.2 xtable_1.7-1 > [[alternative HTML version deleted]]

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ADD COMMENT • link updated 10.7 years ago by Devon Ryan ▴ 200 • written 10.7 years ago by Ed ▴ 230

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Dan Tenenbaum ★ 8.2k

@dan-tenenbaum-4256

Last seen 3.2 years ago

United States

On Thu, Aug 1, 2013 at 3:10 PM, Ed <edforum at="" gmail.com=""> wrote: > Hi there, > > I used the examples in ?gsva and got the following errors on my mac. > However, I run it also on the linux and it worked. > > Please suggest. > > Thanks, > > Weiwei > >> library(limma) >> >> p <- 10 ## number of genes >> n <- 30 ## number of samples >> nGrp1 <- 15 ## number of samples in group 1 >> nGrp2 <- n - nGrp1 ## number of samples in group 2 >> >> ## consider three disjoint gene sets >> geneSets <- list(set1=paste("g", 1:3, sep=""), > + set2=paste("g", 4:6, sep=""), > + set3=paste("g", 7:10, sep="")) >> >> ## sample data from a normal distribution with mean 0 and st.dev. 1 >> y <- matrix(rnorm(n*p), nrow=p, ncol=n, > + dimnames=list(paste("g", 1:p, sep="") , paste("s", 1:n, > sep=""))) >> >> ## genes in set1 are expressed at higher levels in the last 10 samples >> y[geneSets$set1, (nGrp1+1):n] <- y[geneSets$set1, (nGrp1+1):n] + 2 >> >> ## build design matrix >> design <- cbind(sampleGroup1=1, sampleGroup2vs1=c(rep(0, nGrp1), rep(1, > nGrp2))) >> >> ## fit linear model >> fit <- lmFit(y, design) >> >> ## estimate moderated t-statistics >> fit <- eBayes(fit) >> >> ## genes in set1 are differentially expressed >> topTable(fit, coef="sampleGroup2vs1") > ID logFC t P.Value adj.P.Val B > 2 g2 2.43865785 6.79741169 1.490585e-09 1.490585e-08 11.467181 > 1 g1 1.81349993 5.04733755 2.590932e-06 1.295466e-05 4.218446 > 3 g3 1.68971708 4.54930258 1.812937e-05 6.043122e-05 2.348424 > 5 g5 0.25263973 0.65201092 5.161890e-01 9.308575e-01 -6.688660 > 10 g10 0.16766254 0.49082930 6.248376e-01 9.308575e-01 -6.780571 > 9 g9 0.13478444 0.40143265 6.891295e-01 9.308575e-01 -6.820434 > 8 g8 -0.12067327 -0.32614302 7.451340e-01 9.308575e-01 -6.847833 > 7 g7 -0.08002351 -0.23401984 8.155437e-01 9.308575e-01 -6.873660 > 4 g4 0.07875803 0.20538583 8.377717e-01 9.308575e-01 -6.879960 > 6 g6 -0.03196719 -0.08251146 9.344379e-01 9.344379e-01 -6.897676 >> >> ## estimate GSVA enrichment scores for the three sets >> gsva_es <- gsva(y, geneSets, mx.diff=1)$es.obs > | > | 0%The process has forked and you cannot use this > CoreFoundation functionality safely. You MUST exec(). > Break on > __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNC TIONALITY___YOU_MUST_EXEC__() > to debug. > The process has forked and you can > > > >> version > _ > platform x86_64-apple-darwin10.8.0 > arch x86_64 > os darwin10.8.0 > system x86_64, darwin10.8.0 > status > major 3 > minor 0.1 > year 2013 > month 05 > day 16 > svn rev 62743 > language R > version.string R version 3.0.1 (2013-05-16) > nickname Good Sport >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] limma_3.16.7 GSVA_1.8.0 GSEABase_1.22.0 > graph_1.38.3 > [5] annotate_1.38.0 AnnotationDbi_1.22.6 Biobase_2.20.1 > BiocGenerics_0.6.0 > [9] BiocInstaller_1.10.3 > > loaded via a namespace (and not attached): > [1] DBI_0.2-7 grid_3.0.1 IRanges_1.18.2 lattice_0.20-15 > Matrix_1.0-12 > [6] RSQLite_0.11.4 stats4_3.0.1 tools_3.0.1 XML_3.95-0.2 > xtable_1.7-1 >> > I can't reproduce this on a Mac with similar sessionInfo. The differences in sessionInfo() suggest things to try: update the XML package: library(BiocInstaller) biocLite("XML") Locale is also different so that would be another thing to explore if these don't work. Also, you have packages loaded that I do not have loaded. So try starting R as follows: R --vanilla Here is my sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] limma_3.16.7 GSVA_1.8.0 GSEABase_1.22.0 [4] graph_1.38.3 annotate_1.38.0 AnnotationDbi_1.22.6 [7] Biobase_2.20.1 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] DBI_0.2-7 IRanges_1.18.2 RSQLite_0.11.4 XML_3.98-1.1 stats4_3.0.1 [6] tools_3.0.1 xtable_1.7-1 Dan > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD COMMENT • link 10.7 years ago Dan Tenenbaum ★ 8.2k

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Devon Ryan ▴ 200

@devon-ryan-6054

Last seen 8.3 years ago

Germany

Are you running this in R.app or R from the terminal? If the former, try running things from the terminal and see if the problem persists. Some parallel computing related packages (e.g. doMC) will give this error in a GUI. Devon ____________________________________________ Devon Ryan, Ph.D. Email: dpryan at dpryan.com Molecular and Cellular Cognition Lab German Centre for Neurodegenerative Diseases (DZNE) Ludwig-Erhard-Allee 2 53175 Bonn, Germany On Aug 2, 2013, at 12:10 AM, Ed wrote: > Hi there, > > I used the examples in ?gsva and got the following errors on my mac. > However, I run it also on the linux and it worked. > > Please suggest. > > Thanks, > > Weiwei > >> library(limma) >> >> p <- 10 ## number of genes >> n <- 30 ## number of samples >> nGrp1 <- 15 ## number of samples in group 1 >> nGrp2 <- n - nGrp1 ## number of samples in group 2 >> >> ## consider three disjoint gene sets >> geneSets <- list(set1=paste("g", 1:3, sep=""), > + set2=paste("g", 4:6, sep=""), > + set3=paste("g", 7:10, sep="")) >> >> ## sample data from a normal distribution with mean 0 and st.dev. 1 >> y <- matrix(rnorm(n*p), nrow=p, ncol=n, > + dimnames=list(paste("g", 1:p, sep="") , paste("s", 1:n, > sep=""))) >> >> ## genes in set1 are expressed at higher levels in the last 10 samples >> y[geneSets$set1, (nGrp1+1):n] <- y[geneSets$set1, (nGrp1+1):n] + 2 >> >> ## build design matrix >> design <- cbind(sampleGroup1=1, sampleGroup2vs1=c(rep(0, nGrp1), rep(1, > nGrp2))) >> >> ## fit linear model >> fit <- lmFit(y, design) >> >> ## estimate moderated t-statistics >> fit <- eBayes(fit) >> >> ## genes in set1 are differentially expressed >> topTable(fit, coef="sampleGroup2vs1") > ID logFC t P.Value adj.P.Val B > 2 g2 2.43865785 6.79741169 1.490585e-09 1.490585e-08 11.467181 > 1 g1 1.81349993 5.04733755 2.590932e-06 1.295466e-05 4.218446 > 3 g3 1.68971708 4.54930258 1.812937e-05 6.043122e-05 2.348424 > 5 g5 0.25263973 0.65201092 5.161890e-01 9.308575e-01 -6.688660 > 10 g10 0.16766254 0.49082930 6.248376e-01 9.308575e-01 -6.780571 > 9 g9 0.13478444 0.40143265 6.891295e-01 9.308575e-01 -6.820434 > 8 g8 -0.12067327 -0.32614302 7.451340e-01 9.308575e-01 -6.847833 > 7 g7 -0.08002351 -0.23401984 8.155437e-01 9.308575e-01 -6.873660 > 4 g4 0.07875803 0.20538583 8.377717e-01 9.308575e-01 -6.879960 > 6 g6 -0.03196719 -0.08251146 9.344379e-01 9.344379e-01 -6.897676 >> >> ## estimate GSVA enrichment scores for the three sets >> gsva_es <- gsva(y, geneSets, mx.diff=1)$es.obs > | > | 0%The process has forked and you cannot use this > CoreFoundation functionality safely. You MUST exec(). > Break on > __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNC TIONALITY___YOU_MUST_EXEC__() > to debug. > The process has forked and you can > > > >> version > _ > platform x86_64-apple-darwin10.8.0 > arch x86_64 > os darwin10.8.0 > system x86_64, darwin10.8.0 > status > major 3 > minor 0.1 > year 2013 > month 05 > day 16 > svn rev 62743 > language R > version.string R version 3.0.1 (2013-05-16) > nickname Good Sport >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] limma_3.16.7 GSVA_1.8.0 GSEABase_1.22.0 > graph_1.38.3 > [5] annotate_1.38.0 AnnotationDbi_1.22.6 Biobase_2.20.1 > BiocGenerics_0.6.0 > [9] BiocInstaller_1.10.3 > > loaded via a namespace (and not attached): > [1] DBI_0.2-7 grid_3.0.1 IRanges_1.18.2 lattice_0.20-15 > Matrix_1.0-12 > [6] RSQLite_0.11.4 stats4_3.0.1 tools_3.0.1 XML_3.95-0.2 > xtable_1.7-1 >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

ADD COMMENT • link 10.7 years ago Devon Ryan ▴ 200

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It is probably the GUI, the error seems to come from CoreFoundation which is a Mac GUI framework On Thu, Aug 1, 2013 at 6:33 PM, Devon Ryan <dpryan@dpryan.com> wrote: > Are you running this in R.app or R from the terminal? If the former, try > running things from the terminal and see if the problem persists. Some > parallel computing related packages (e.g. doMC) will give this error in a > GUI. > > Devon > > ____________________________________________ > Devon Ryan, Ph.D. > Email: dpryan@dpryan.com > Molecular and Cellular Cognition Lab > German Centre for Neurodegenerative Diseases (DZNE) > Ludwig-Erhard-Allee 2 > 53175 Bonn, Germany > > On Aug 2, 2013, at 12:10 AM, Ed wrote: > > > Hi there, > > > > I used the examples in ?gsva and got the following errors on my mac. > > However, I run it also on the linux and it worked. > > > > Please suggest. > > > > Thanks, > > > > Weiwei > > > >> library(limma) > >> > >> p <- 10 ## number of genes > >> n <- 30 ## number of samples > >> nGrp1 <- 15 ## number of samples in group 1 > >> nGrp2 <- n - nGrp1 ## number of samples in group 2 > >> > >> ## consider three disjoint gene sets > >> geneSets <- list(set1=paste("g", 1:3, sep=""), > > + set2=paste("g", 4:6, sep=""), > > + set3=paste("g", 7:10, sep="")) > >> > >> ## sample data from a normal distribution with mean 0 and st.dev. 1 > >> y <- matrix(rnorm(n*p), nrow=p, ncol=n, > > + dimnames=list(paste("g", 1:p, sep="") , paste("s", 1:n, > > sep=""))) > >> > >> ## genes in set1 are expressed at higher levels in the last 10 samples > >> y[geneSets$set1, (nGrp1+1):n] <- y[geneSets$set1, (nGrp1+1):n] + 2 > >> > >> ## build design matrix > >> design <- cbind(sampleGroup1=1, sampleGroup2vs1=c(rep(0, nGrp1), rep(1, > > nGrp2))) > >> > >> ## fit linear model > >> fit <- lmFit(y, design) > >> > >> ## estimate moderated t-statistics > >> fit <- eBayes(fit) > >> > >> ## genes in set1 are differentially expressed > >> topTable(fit, coef="sampleGroup2vs1") > > ID logFC t P.Value adj.P.Val B > > 2 g2 2.43865785 6.79741169 1.490585e-09 1.490585e-08 11.467181 > > 1 g1 1.81349993 5.04733755 2.590932e-06 1.295466e-05 4.218446 > > 3 g3 1.68971708 4.54930258 1.812937e-05 6.043122e-05 2.348424 > > 5 g5 0.25263973 0.65201092 5.161890e-01 9.308575e-01 -6.688660 > > 10 g10 0.16766254 0.49082930 6.248376e-01 9.308575e-01 -6.780571 > > 9 g9 0.13478444 0.40143265 6.891295e-01 9.308575e-01 -6.820434 > > 8 g8 -0.12067327 -0.32614302 7.451340e-01 9.308575e-01 -6.847833 > > 7 g7 -0.08002351 -0.23401984 8.155437e-01 9.308575e-01 -6.873660 > > 4 g4 0.07875803 0.20538583 8.377717e-01 9.308575e-01 -6.879960 > > 6 g6 -0.03196719 -0.08251146 9.344379e-01 9.344379e-01 -6.897676 > >> > >> ## estimate GSVA enrichment scores for the three sets > >> gsva_es <- gsva(y, geneSets, mx.diff=1)$es.obs > > | > > | 0%The process has forked and you cannot use this > > CoreFoundation functionality safely. You MUST exec(). > > Break on > > > __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATION_FUNC TIONALITY___YOU_MUST_EXEC__() > > to debug. > > The process has forked and you can > > > > > > > >> version > > _ > > platform x86_64-apple-darwin10.8.0 > > arch x86_64 > > os darwin10.8.0 > > system x86_64, darwin10.8.0 > > status > > major 3 > > minor 0.1 > > year 2013 > > month 05 > > day 16 > > svn rev 62743 > > language R > > version.string R version 3.0.1 (2013-05-16) > > nickname Good Sport > >> sessionInfo() > > R version 3.0.1 (2013-05-16) > > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets methods > > base > > > > other attached packages: > > [1] limma_3.16.7 GSVA_1.8.0 GSEABase_1.22.0 > > graph_1.38.3 > > [5] annotate_1.38.0 AnnotationDbi_1.22.6 Biobase_2.20.1 > > BiocGenerics_0.6.0 > > [9] BiocInstaller_1.10.3 > > > > loaded via a namespace (and not attached): > > [1] DBI_0.2-7 grid_3.0.1 IRanges_1.18.2 lattice_0.20-15 > > Matrix_1.0-12 > > [6] RSQLite_0.11.4 stats4_3.0.1 tools_3.0.1 XML_3.95-0.2 > > xtable_1.7-1 > >> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

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