[BioC] HTSanalyzeR GSEA Error

[Dario Strbenac]

Hello,

I'm trying to do GSEA with the HTSanalyzeR package and I get a non-descriptive error message.

Here is the important part of the code :

sets.curated <- getGmt("c2.all.v3.0.entrez.gmt")
gsca <- new("GSCA", listOfGeneSetCollections=list(MsigDB=sets.curated), geneList=scores, hits=genes.use)
gsca <- preprocess(gsca, species = "Hs", initialIDs = "Entrez.gene")
gsca <- analyze(gsca, para = list(pValueCutoff = 0.05, pAdjustMethod = "BH", nPermutations = 100, minGeneSetSize = 10, exponent = 1))

When I call analyze() I get an internal error :

-Performing hypergeometric analysis ...
Error in as.vector(x) : no method for coercing this S4 class to a vector

my gsca object can be downloaded from : http://129.94.136.7/file_dump/dario/gsca.obj

> head(scores)
   643837    148398    339451     84069      9636    375790 
0.2191336 0.1679645 0.2565248 0.6424748 0.3201527 0.2340810 
> head(genes.use)
[1] "55966"  "249"    "2048"   "9473"   "80149"  "353500"

Also, it would be nice if the hits vector isn't mandatory. Figure 1 of the vignette says the package can be used for " (ii) gene set enrichment analysis (GSEA) for concordant trends of a gene set in one phenotype." However, it seems to be only for designed for genetic screens ("(i) hypergeometric tests for overlap between hits and gene sets"), as not giving a hits vector produces an error.

> gsca <- new("GSCA", listOfGeneSetCollections=list(MsigDB=sets.curated), geneList=scores)
Error in is.character(para) : 'para' is missing

I'm using HTSanalyzeR_2.6.0 in R 2.14.0.

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia