[GSVA] Segfault with GSVA
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Robert Castelo ★ 2.7k
@rcastelo
Last seen 29 days ago
Barcelona/Universitat Pompeu Fabra
hi Luca, and everybody else, the original post was not published at the list but i'm posting it below with the solution to the problem. the problem that is causing the segfault is, next to a bad handling of the error, the fact that some genes have a constant expression value across all samples, leading to no variability: dim(matrix) [1] 999 10 sdsgenes <- apply(matrix, 1, sd) summary(sdsgenes) Min. 1st Qu. Median Mean 3rd Qu. Max. 0.00000 0.00000 0.01776 0.10120 0.10220 2.83900 sum(sdsgenes == 0) [1] 320 as you can see, 320 out of the 999 have standard deviation zero, if you do the calculations filtering those genes out, things will work: x <- gsva(expr=matrix[sdsgenes > 0, ], gset.idx.list=idx.list) Estimating GSVA scores for 152 gene sets. Computing observed enrichment scores Estimating ECDFs in microarray data with Gaussian kernels Using parallel with 12 cores |===================================================================== ==========================| 100% dim(x$es.obs) [1] 152 10 i have added a QC that removes upfront all genes with zero standard deviation, reporting this action when the argument verbose=TRUE. this has been fixed in both GSVA release version 1.6.2 and development version 1.7.5 which should be available at the BioC site within the next 48 hrs. thanks for the bug reporting!! robert. On 01/16/2013 11:49 AM, Luca Beltrame wrote: > Hello, > > I'm a bioinformatician working in a no profit research institute, and recently > I've been using GSVA in a number of pipelines. However, with some data sets > (in particular Affymetrix arrays) I encounter a segfault in the C code > outlined below. > > I attached to this mail a section of a matrix that reproduces the problem: > mouse data, normalized with GCRMA and annotated using M.Dai's custom CDFs. > > Thanks in advance. > > Test case below: > >> library(GSVA) >> library(GSVAdata) >> data(c2BroadSets) >> matrix = as.matrix(read.delim("matrix.txt", row.names=1)) # Mouse data >> idx.list = geneIds(c2BroadSets) # convert to regular list >> gsva(expr=matrix, gset.idx.list=idx.list) > Estimating GSVA scores for 269 gene sets. > Computing observed enrichment scores > Estimating ECDFs in microarray data with Gaussian kernels > > *** caught segfault *** > address 0x7fa467060140, cause 'memory not mapped' > > Traceback: > 1: .C("matrix_density_R", as.double(t(expr[, sample.idxs])), > as.double(t(expr)), R = double(n.test.samples * n.genes), > n.density.samples, n.test.samples, n.genes, as.integer(rnaseq)) > 2: compute.gene.density(expr, sample.idxs, rnaseq, kernel) > 3: compute.geneset.es(expr, gset.idx.list, 1:n.samples, rnaseq = rnaseq, > abs.ranking = abs.ranking, parallel.sz = parallel.sz, parallel.type = > parallel.type, mx.diff = mx.diff, tau = tau, kernel = kernel, verbose = > verbose) > 4: GSVA:::.gsva(expr, mapped.gset.idx.list, method, rnaseq, abs.ranking, > no.bootstraps, bootstrap.percent, parallel.sz, parallel.type, mx.diff, > tau, kernel, verbose) > 5: .local(expr, gset.idx.list, annotation, ...) > 6: gsva(expr = matr, gset.idx.list = geneIds(c2BroadSets)) > 7: gsva(expr = matr, gset.idx.list = geneIds(c2BroadSets)) > >> sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-suse-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C > [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8 > [5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=it_IT.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GSVA_1.6.1 GSEABase_1.20.1 graph_1.36.1 > [4] annotate_1.36.0 AnnotationDbi_1.20.3 Biobase_2.18.0 > [7] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] DBI_0.2-5 IRanges_1.16.4 parallel_2.15.2 RSQLite_0.11.2 > [5] stats4_2.15.2 tools_2.15.2 XML_3.95-0.1 xtable_1.7-1 > > -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 fax: +34.933.160.550
RNASeq Microarray Annotation gcrma convert GSVA RNASeq Microarray Annotation gcrma GSVA • 2.0k views
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capricy gao ▴ 230
@capricy-gao-5298
Last seen 7.1 years ago
I am trying to install AnnotationForge package on my linux system and got the following message: ____________________ > source("http://bioconductor.org/biocLite.R") > biocLite("AnnotationForge") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.9. Installing package(s) 'AnnotationForge' Warning messages: 1: package ‘AnnotationForge’ is not available (for R version 2.15.1) 2: installed directory not writable, cannot update packages 'AnnotationDbi',   'Biobase', 'Biostrings', 'Cairo', 'DNAcopy', 'GenomeGraphs', 'Hmisc',   'IRanges', 'RColorBrewer', 'RCurl', 'RSQLite', 'SKAT', 'XML', 'affy',   'affyio', 'annotate', 'biomaRt', 'bitops', 'caTools', 'colorspace', 'digest',   'doMC', 'fastcluster', 'flexmix', 'foreach', 'fpc', 'gcrma', 'gdata',   'genefilter', 'ggplot2', 'gplots', 'gtools', 'h5r', 'igraph', 'iterators',   'lumi', 'mclust', 'methylumi', 'modeltools', 'multcomp', 'multicore',   'mvtnorm', 'plotrix', 'plyr', 'preprocessCore', 'proto', 'reshape2',   'scatterplot3d', 'stringr', 'xtable', 'KernSmooth', 'MASS', 'Matrix', 'boot',   'class', 'cluster', 'codetools', 'foreign', 'lattice', 'mgcv', 'nlme',   'nnet', 'rpart', 'spatial', 'survival' ------------------------------------------------ All other packages such as edgeR, DESeq... are fine. This is the first time I met this kind of problem... Anybody could help me out? Thanks. [[alternative HTML version deleted]]
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Hi Capricy Gao, On 1/16/2013 10:58 AM, capricy gao wrote: > I am trying to install AnnotationForge package on my linux system and got the following message: > > ____________________ > >> source("http://bioconductor.org/biocLite.R") >> biocLite("AnnotationForge") > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.9. > Installing package(s) 'AnnotationForge' > Warning messages: > 1: package ???AnnotationForge??? is not available (for R version 2.15.1) > 2: installed directory not writable, cannot update packages 'AnnotationDbi', > ? 'Biobase', 'Biostrings', 'Cairo', 'DNAcopy', 'GenomeGraphs', 'Hmisc', > ? 'IRanges', 'RColorBrewer', 'RCurl', 'RSQLite', 'SKAT', 'XML', 'affy', > ? 'affyio', 'annotate', 'biomaRt', 'bitops', 'caTools', 'colorspace', 'digest', > ? 'doMC', 'fastcluster', 'flexmix', 'foreach', 'fpc', 'gcrma', 'gdata', > ? 'genefilter', 'ggplot2', 'gplots', 'gtools', 'h5r', 'igraph', 'iterators', > ? 'lumi', 'mclust', 'methylumi', 'modeltools', 'multcomp', 'multicore', > ? 'mvtnorm', 'plotrix', 'plyr', 'preprocessCore', 'proto', 'reshape2', > ? 'scatterplot3d', 'stringr', 'xtable', 'KernSmooth', 'MASS', 'Matrix', 'boot', > ? 'class', 'cluster', 'codetools', 'foreign', 'lattice', 'mgcv', 'nlme', > ? 'nnet', 'rpart', 'spatial', 'survival' > ------------------------------------------------ > > All other packages such as edgeR, DESeq... are fine. This is the first time I met this kind of problem... > > Anybody could help me out? Thanks. You are using BiocInstaller version 1.4.9, which implies that you are installing BioC version 2.10. This version didn't have AnnotationForge. If you want to upgrade, then follow the instructions on the install page of the BioC website: |source("http://bioconductor.org/biocLite.R") biocLite("BiocUpgrade") Best, Jim | > [[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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Thank you very much for the email. It works fine now. ________________________________ From: James W. MacDonald <jmacdon@uw.edu> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> Sent: Wednesday, January 16, 2013 10:13 AM Subject: Re: [BioC] ‘AnnotationForge’ is not available for Linux system?? Hi Capricy Gao, On 1/16/2013 10:58 AM, capricy gao wrote: > I am trying to install AnnotationForge package on my linux system and got the following message: > > ____________________ > >> source("http://bioconductor.org/biocLite.R") >> biocLite("AnnotationForge") > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.9. > Installing package(s) 'AnnotationForge' > Warning messages: > 1: package ‘AnnotationForge’ is not available (for R version 2.15.1) > 2: installed directory not writable, cannot update packages 'AnnotationDbi', >   'Biobase', 'Biostrings', 'Cairo', 'DNAcopy', 'GenomeGraphs', 'Hmisc', >   'IRanges', 'RColorBrewer', 'RCurl', 'RSQLite', 'SKAT', 'XML', 'affy', >   'affyio', 'annotate', 'biomaRt', 'bitops', 'caTools', 'colorspace', 'digest', >   'doMC', 'fastcluster', 'flexmix', 'foreach', 'fpc', 'gcrma', 'gdata', >   'genefilter', 'ggplot2', 'gplots', 'gtools', 'h5r', 'igraph', 'iterators', >   'lumi', 'mclust', 'methylumi', 'modeltools', 'multcomp', 'multicore', >   'mvtnorm', 'plotrix', 'plyr', 'preprocessCore', 'proto', 'reshape2', >   'scatterplot3d', 'stringr', 'xtable', 'KernSmooth', 'MASS', 'Matrix', 'boot', >   'class', 'cluster', 'codetools', 'foreign', 'lattice', 'mgcv', 'nlme', >   'nnet', 'rpart', 'spatial', 'survival' > ------------------------------------------------ > > All other packages such as edgeR, DESeq... are fine. This is the first time I met this kind of problem... > > Anybody could help me out? Thanks. You are using BiocInstaller version 1.4.9, which implies that you are installing BioC version 2.10. This version didn't have AnnotationForge. If you want to upgrade, then follow the instructions on the install page of the BioC website: |source("http://bioconductor.org/biocLite.R") biocLite("BiocUpgrade") Best, Jim | >     [[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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]
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