Hello, I don't understand why TopGO wouldn't work with gene symbols GOdata <- new("topGOdata", ontology = GOcategory, allGenes = allGenes, annotationFun = annFUN.org, nodeSize = 10, mapping = "org.Hs.eg.db", ID = "symbol") test <- new("classicCount", testStatistic = GOFisherTest) testResult <- getSigGroups(GOdata, test) Gives as a result : -- Classic Algorithm -- the algorithm is scoring 0 nontrivial nodes parameters: test statistic: Note that allGenes is I have topGO_2.12.0 and R 3.0.1 -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

Sorry for the incomplete e-mail. Annoying Microsoft Outlook Web App keyboard shortcuts are to blame. I wish universities had stuck to Mirapoint webmail. allGenes is : head(allGenes) DDX11L1 WASH7P MIR1302-2 FAM138A AL627309.2 OR4G11P FALSE FALSE FALSE FALSE FALSE FALSE Levels: FALSE TRUE table(allGenes) allGenes FALSE TRUE 57230 51