[BioC] SeqGSEA skip DS portion
SeqGSEA user [guest]
guest at bioconductor.org
Wed Jul 10 20:25:21 CEST 2013
Can we skip the DS calculation part of GSEA and perform enrichment using on the DE portion?
I tried to do this, but I'm getting some error messages which I cannot intepret. Please see my code and error messages below. Also, I only have 2 groups and 2 samples per group. Any advice on what these warnings and error messages mean will be appreciated!
Thanks!
Code:
# gene set file
geneset.file <- system.file("extdata", "gs_symb.txt", package="SeqGSEA", mustWork=TRUE)
counts <- loadExonCountData(ps.files, cb.files)
# remove genes with low exprssion
#RCS <- exonTestability(RCS, cutoff=5)
counts <- exonTestability(counts, cutoff=5)
geneTestable <- geneTestability(counts)
counts <- subsetByGenes(counts, unique(geneID(counts))[ geneTestable ])
# get gene IDs, which will be used in initialization of gene set
geneIDs <- unique(geneID(counts))
# load gene set data
> gene.set <- loadGenesets(geneset.file, geneIDs, geneID.type="ensembl", genesetsize.min = 5, genesetsize.max = 1000)
Warning message:
In max(unlist(GS)) : no non-missing arguments to max; returning -Inf
> gene.set <- GSEnrichAnalyze(gene.set, DEscore, DEscore.perm, weighted.type=1)
Error: all(i <= size(x)) is not TRUE
-- output of sessionInfo():
-- output of sessionInfo():
> sessionInfo()
R version 3.0.0 (2013-04-03)
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] SeqGSEA_1.0.2 foreach_1.4.1 biomaRt_2.16.0 DESeq_1.12.0 lattice_0.20-15 locfit_1.5-9.1 Biobase_2.20.0
[8] BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] annotate_1.38.0 AnnotationDbi_1.22.6 codetools_0.2-8 compiler_3.0.0 DBI_0.2-7 doParallel_1.0.3
[7] genefilter_1.42.0 geneplotter_1.38.0 grid_3.0.0 IRanges_1.18.1 iterators_1.0.6 RColorBrewer_1.0-5
[13] RCurl_1.95-4.1 RSQLite_0.11.4 splines_3.0.0 stats4_3.0.0 survival_2.37-4 tools_3.0.0
[19] XML_3.95-0.2 xtable_1.7-1
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