[BioC] HTSanalyzeR GSEA Error

[Xin Wang]

Hello Dario,

[Don't know if it is the right way to reply to bioc list. My first time posting a message here.]

First of all, thanks very much for using HTSanalyzeR, and for posting an error when using it. 

Taking a careful look at your code, you would find that the argument 'listOfGeneSetCollections' is supposed to accept a list of  gene set collections (each gene set collection is a list of gene sets). 
Thus, you need to do this:

sets.curated <- getGmt("c2.all.v3.0.entrez.gmt")
##convert to a list of gene sets
c2<-geneIds(sets.curated)
##create an object of 'GSCA'
gsca <- new("GSCA", listOfGeneSetCollections=list(MsigDB=c2), 
geneList=scores, hits=genes.use)

Then probably you will not get any error when running 'preprocess' and 'analyze'.

Please do read the '?GSCA' and 'Appendix B' of the Vignette! Let me know if you still have a problem.

Best wishes,

Xin

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