Hi BioC, For 3 experimental groups in LIMMA, when vennDiagram is generated based on : mask <- c(1,1,1,2,2,3,3,3); design <- model.matrix(~ -1+factor(mask)); colnames(design) <- c("Group1","Group2","Group3"); ConX<-as.matrix(c("Group1-Group2","Group1-Group3","Group2-Group3")); fit2 <- contrasts.fit(fit,contrast.matrix); fit2 <- eBayes(fit2); ConRow <- nrow(ConX); #now I am extracting all DE genes from each contrast and collect it in array, so, later I can draw heatmap but I have lots of probesets co in that array for(i in 1:ConRow) { DEtable <- topTable(fit2,coef = i,number = numberDE,adjust = "fdr",sort.by = "P"); DEList[i] <- list(DEtable); AllDEGenes <- c(AllDEGenes,as.character(DEList[[i]][,"ID"])); AllDE_FDR <- c(AllDE_FDR,as.character(DEList[[i]][,"P.Value"])); } For 3 experimental groups, how can someone extract differentially expressed genes which is common in all three groups? Is it possible to generate vennDiagram() for more than 3 groups..in LIMMA? Thank you in advance, Saurin