Dear all:
I'm a new R user but attempted to use GSVA to analyze a RNAseq gene read count table downloaded from GTEx (http://www.gtexportal.org/home/). I have previously used GSVA to analyze Affymetrix data without issue, but I have no clue about the issue encountered when analyzing the RNAseq read count table (annotation issue, maybe???). For preprocessing, I normalized using DEseq (LogGeoMean), and filtered out genes with low count. The gene IDs are Ensemble ID such as ENSG00000227232. Here is the info for the expressionset I made:
> ExprSetName ExpressionSet (storageMode: lockedEnvironment) assayData: 20831 features, 187 samples element names: exprs protocolData: none phenoData sampleNames: GTEX.N7MS.0007.SM.2D7W1 GTEX.N7MT.0007.SM.3GACQ ... GTEX.Y8E5.0006.SM.47JWQ (187 total) varLabels: SUBJID GENDER ... ScaleFactor (9 total) varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: org.Hs.eg.db
However, when I tried to run GSVA, the resulting gene set list is empty with the following message:
> traceback() 5: stop("The gene set list is empty! Filter may be too stringent.") 4: GSVA:::.gsva(exprs(expr), mapped.gset.idx.list, method, rnaseq, abs.ranking, no.bootstraps, bootstrap.percent, parallel.sz, parallel.type, mx.diff, tau, kernel, verbose) 3: .local(expr, gset.idx.list, annotation, ...) 2: gsva(ExprSetName, c2BroadSets, rnaseq = TRUE, abs.ranking = FALSE, min.sz = 1, max.sz = 1000, mx.diff = TRUE, parallel.sz = 2) 1: gsva(ExprSetName, c2BroadSets, rnaseq = TRUE, abs.ranking = FALSE, min.sz = 1, max.sz = 1000, mx.diff = TRUE, parallel.sz = 2)
The following is my session info:
> sessionInfo() R version 3.1.1 (2014-07-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] GSVAdata_0.99.11 hgu95a.db_2.10.1 BiocInstaller_1.12.1 genefilter_1.44.0 GSVA_1.10.3 GSEABase_1.24.0 graph_1.40.1 annotate_1.40.1 org.Hs.eg.db_2.10.1 [10] RSQLite_0.11.4 DBI_0.3.1 AnnotationDbi_1.24.0 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] IRanges_1.20.7 splines_3.1.1 stats4_3.1.1 survival_2.37-7 tools_3.1.1 XML_3.98-1.1 xtable_1.7-4 > packageDescription('GSVA')$Maintainer [1] "Justin Guinney <justin.guinney@sagebase.org>"
Thank you :)