Dear Mark, If I understand your problem correctly, neither GSEA nor GSA will accomodate it. The only option I know of is geneSetTest() in the limma package. This generally works well, although it will give you someone over optimistic p-values if there are strong positive correlations between the genes in your gene sets. Best wishes Gordon >Date: Fri, 02 Mar 2007 12:04:09 -0500 >From: Mark W Kimpel <mwkimpel at="" gmail.com=""> >Subject: [BioC] GSEA with one class metaanalysis >To: Bioconductor Newsgroup <bioconductor at="" stat.math.ethz.ch=""> > >I am in the process of performing a meta-analysis on multiple MA studies >run on several platforms and several species. Although I realize there >are probably other ways to approach the data, my collaborators have >chosen to use Cohen's D-statistic to summarize their data. > >I would like to use GSEA to look for over-represented groups or pathways >in the data, but what I will end up with is essentially a one-class >experiment. In other words, I would like to identify groups whose >summary D-statistic (I recognize from the recent literature that there >is more than one summary method available) is different from zero. > > From what I have read, the GSEA method is usually used to evaluate 2 >class data, the GSA method of Tibshurani can be used to evaluate >multi-class data, but can either method be easily adapted to evaluate >one class data? It would seem theoretically reasonable, but I don't know >if I would have to modify one of the packages or if one already provides >for this. > >And, while I'm at it, I will also want to look for individual genes >whose average D-statistic is different from zero. I am advocating using >a t-test with n=number of experiments with corresponding degrees of >freedom, whereas others are advocating using a z-test because the >D-statistics are summarizing many underlying individual statistics. > >Help with these questions would be deeply appreciated. > >Mark > >-- >Mark W. Kimpel MD >Neuroinformatics >Department of Psychiatry >Indiana University School of Medicine