[BioC] romer in limma question
iaingallagher at btopenworld.com
Tue Nov 9 14:39:09 CET 2010
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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