Hi there, I'm trying to use the hyperGTest function. What I tried is as follows: > params <- new("GOHyperGParams", geneIds = GList, universeGeneIds = geneUniverse, annotation = "hgu133plus2", ontology = "BP", pvalueCutoff = hgCutoff, conditional = FALSE,testDirection = "over") Both GList & geneUniverse contain genes in HUGO format (symbols). This part seems to compute fine. But when I try the next part, it gives me an error: > hgOver <- hyperGTest(params) Error in getUniverseHelper(probes, lib, entrezIds) : No Entrez Gene ids left in universe Is this because I used HUGO symbols & not EntrezIDs? I couldnt understand what exactly the error means. Any information about this would be appreciated. Thanks Vivek Kaimal

Hi, "Vivek Kaimal" <vivek.kaimal at="" cchmc.org=""> writes: > Hi there, > > I'm trying to use the hyperGTest function. What I tried is as > follows: > >> params <- new("GOHyperGParams", geneIds = GList, universeGeneIds = > geneUniverse, annotation = "hgu133plus2", ontology = "BP", pvalueCutoff > = hgCutoff, conditional = FALSE,testDirection = "over") > > Both GList & geneUniverse contain genes in HUGO format (symbols). You need to use Entrez IDs for the geneIds and universeGeneIds argument. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org