Hi, I'm trying to reproduce results I got from DAVID (http://david.abcc.ncifcrf.gov/) using topGO. For the GO MF category, the top 10 terms I get from topGO are basically the same as DAVID but the p-values are drastically different. I'm using a named factor (intGenes) to define my "interesting" and "uninteresting" gene symbols and as my microarray doesn't have an annotation I'm using "org.Hs.eg.db", then my code is as follows: GOdata <- new("topGOdata", ontology = "MF", allGenes = intGenes, annot = annFUN.org, mapping = "org.Hs.eg.db", ID="symbol", nodeSize=20) test.stat <- new("classicCount", testStatistic = GOFisherTest, name = "Fisher test") resultFisher <- getSigGroups(GOdata, test.stat) allRes <- GenTable(GOdata, classic = resultFisher, orderBy = "classic", ranksOf = "classic", topNodes = 10) My top result in DAVID has a fisher exact p-value of .006, but in "allRes" the same term (Term=sequence-specific DNA binding, annotated=518, significant=41, expected=18.92) only has a p-value of .31 (in the column labeled "classic"). Manually plugging the numbers into fishers.test() it looks like DAVID is much closer to what the p-value should be. Can anyone point me to where I've gone wrong with topGO cause I think I've followed the instructions correctly!? Thanks, Paul. -- Paul Geeleher (PhD Student) School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com