>Date: Tue, 18 Sep 2007 17:40:26 -0400 (EDT) >From: Brooke LaFlamme <bal44 at="" cornell.edu=""> >Subject: [BioC] topTable in limma >To: bioconductor at stat.math.ethz.ch > >Sorry, I had one more question! > >If I have more that one contrast in my fit (after running >ebayes(fit)), and I use this to produce a table of top genes using >topTable(), does the list of genes produced simply correspond to the >genes with the highest probability of being significant in one or >more contrasts, up to N genes? If you specify a particular contrast, topTable will rank by p-values and B-statistics for that contrast. If you don't, it will rank on F-statistics, which is a test of overall significance for all (one or more of) the contrasts. Best wishes Gordon >This is what I assumed to be the case, but I'm not certain. > >Thanks again! > >Brooke L.