SeqGSEA skip DS portion
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Guest User ★ 13k
@guest-user-4897
Last seen 9.6 years ago
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(): > 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 -- Sent via the guest posting facility at bioconductor.org.
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Entering edit mode
Guest User ★ 13k
@guest-user-4897
Last seen 9.6 years ago
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 -- Sent via the guest posting facility at bioconductor.org.
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Hi, The answer to your first question is YES. However, the error you encountered wasn't caused by your skipping the DS portion. I am not sure what species you were working on and what were your gene IDs. Regards Xi On Thu, Jul 11, 2013 at 2:25 AM, SeqGSEA user [guest] < guest@bioconductor.org> wrote: > > 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 > > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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