To get a venn diagram for three lists of genes use the following code library(limma) list1 <-list of probe ID list2 <-list of probe ID list3 <-list of probe ID dooby.all <- union(list1,union(list2,list3)) dooby.mat <- matrix(0,nrow=length(dooby.all),ncol=3) colnames(dooby.mat) <- c("list1","list2","list3") for (i in 1:length(dooby.all)) { dooby.mat[i,1] <- dooby.all[i]%in%list1 dooby.mat[i,2] <- dooby.all[i]%in%list2 dooby.mat[i,3] <- dooby.all[i]%in%list3} dooby.ven <- vennCounts(dooby.mat) vennDiagram(dooby.ven) -- ______________________________________________ Anthony Bosco - PhD Student Institute for Child Health Research (Company Limited by Guarantee ACN 009 278 755) Subiaco, Western Australia, 6008 Ph 61 8 9489 , Fax 61 8 9489 7700 email anthonyb@ichr.uwa.edu.au