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.
>

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