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? e.g. symbols <- unlist(mget(featureNames(rmaData)) if rmaData is my normalised expression set. Then symbolsOfficial <- alias2SymbolTable(symbols,species="Hs") #get the genesets load("human_c2.rdata") #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. iain

Hi Iain, c2 is your first input in romer, which is "iset". Suppose unlist(mget(featureNames(rmaData)) give you the gene symbols of your data, alias2SymbolTable converts these symbols to official gene symbols in the same order as in your rmaData. Then, symbols2indices allow to get the indexfrom your data for C2 gene sets. Probably, an extra step will be needed to make sure none of the gene sets are empty after matching to your data. c2i<-c2[which(unlist(lapply(c2, length))!=0)] In this case, c2i is the first input in romer, which is "iset". Hope this help. Good luck. Di On Wed, Nov 10, 2010 at 12:39 AM, Iain Gallagher < iaingallagher@btopenworld.com> wrote: > 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? > > e.g. > > symbols <- unlist(mget(featureNames(rmaData)) > > if rmaData is my normalised expression set. Then > > symbolsOfficial <- alias2SymbolTable(symbols,species="Hs") > > #get the genesets > load("human_c2.rdata") > #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. > > iain > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]