Hi, This might be simple question, but I am confused somehow..if anyone can guide me through this that would be great. > fit<- eBayes(fit); > results_fdr1<- classifyTestsP(fit, p.value=0.01, method="fdr") > vennDiagram(results_fdr1,include = "both"); (I get very nice vennDiagram, my all contrasts have nice numbers of genes) > coef1_Genes <- topTable(fit,coef = 1, adjust = "fdr",number = 50); Above when I get coef1_Genes, which has adjusted P.value way higher than 0.01, sometimes its range from 0.5.....0.904 or something like that. so, how can I decide my cutoff for FDR? I saw nice numbers in my vennDiagram above so, i thought I have lots of genes which has < 0.01 FDR but it not when I checked in coef1_Genes. In above results coef1_Genes P.value = FDR cutoff right? There is no option in topTable for howmuch FDR level..! I set p.value = 0.01 in classifyTestsP function so, I think classifyTestsP gives me FDR level < 0.01, because I am using method = "fdr", and those nice number I see in vennDiagram.......Is this right understanding? if yes then how can I access those genes? Please, let me know, I highly appreciate your help in advance. Thank you, Saurin ===== Saurin's WebWorld: http://hawkmail.monmouth.edu/~s0451884