[BioC] HTSanalyzeR GSEA Error

Dario Strbenac D.Strbenac at garvan.org.au
Fri Nov 18 02:00:07 CET 2011

Thanks. It works now.

---- Original message ----
>Date: Thu, 17 Nov 2011 16:14:46 +0000
>From: Xin Wang <Xin.Wang at cancer.org.uk>  
>Subject: Re: [BioC] HTSanalyzeR GSEA Error  
>To: "D.Strbenac at garvan.org.au" <D.Strbenac at garvan.org.au>
>Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>
>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
>##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,
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Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010

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