Dear colleagues, Using Bioconductor-R, I would like to make venn diagrams based on two lists of Affy-geneIDs (of different length). In fact I would like to know which genes are present in both lists and which not. Best regards, Thank you in advance!!! Katleen De Preter -- No virus found in this outgoing message. Checked by AVG Anti-Virus.

Dear Katleen, I have been doing this recently in, probably, quite a simplistic way using 'intersect()' and 'setdiff()' to find the genes common to both lists, or belonging to just one of the lists. This gave me the required gene lists and I then made a venn diagram (for illustration) using PowerPoint. Kind regards, Laura ....... Laura E Hollins PhD Student Gene Therapy and Bioinformatics Groups Paterson Institute for Cancer Research email: LHollins@PICR.man.ac.uk -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Katleen De Preter Sent: 18 January 2005 09:12 To: bioconductor@stat.math.ethz.ch Subject: [BioC] venn diagram Dear colleagues, Using Bioconductor-R, I would like to make venn diagrams based on two lists of Affy-geneIDs (of different length). In fact I would like to know which genes are present in both lists and which not. Best regards, Thank you in advance!!! Katleen De Preter -- No virus found in this outgoing message. Checked by AVG Anti-Virus. _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

list1, list2, and list3 are lists of Affymetrix probe IDs (lists can be of any length). library(limma) 2-way venn diagram list1 list2 dooby.all <- union(list1,list2)) dooby.mat <- matrix(0,nrow=length(dooby.all),ncol=2) colnames(dooby.mat) <- c("list1","list2") 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.ven <- vennCounts(dooby.mat) vennDiagram(dooby.ven) 3-way venn list1 list2 list3 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