[BioC] SeqGSEA skip DS portion

[SeqGSEA user [guest]]

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        


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