[BioC] romer in limma question

Iain Gallagher iaingallagher at btopenworld.com
Tue Nov 9 14:39:09 CET 2010

Hello list

I'm being a bit stupid with romer (for GSEA) in the limma suite. In order to run the analysis I need to indicate in each gene set I have which row in my expression data that gene belongs to.

I can see that this involves using symbols2indices. Is the best was forward to simply reannotate the feature names of my expression data as symbols and then run symbols2indices?


symbols <- unlist(mget(featureNames(rmaData))

if rmaData is my normalised expression set. Then

symbolsOfficial <- alias2SymbolTable(symbols,species="Hs")

#get the genesets
#ok now set up the index of where these genes are in the genesets
c2 = symbols2indices(Hs.gmtl.c2, symbols)

Is the c2 object now my first input to romer?

Thanks for any advice.


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