I asked this a while ago, but didn't get any further ... I built an annotation package for a mouse IPI database using "AnnotationDbi" (IPI.MOUSE.3.37.20080509.db) and am now putting it to use with "hyperGTests" from "GOstats". The annotation package mapps all IPI IDs as "probes" to the relevant annotation data and I thought it should be possible to hand "geneIds" and universeGeneIds in the form of probe names (here IPI IDs) to the hyperGTest function. If I do so I always get the error: # Error in getUniverseHelper(probes, datPkg, entrezIds) : # No Entrez Gene ids left in universe If I use the annotation package to pre-convert the probes (IPI IDs) into entrez-IDs everything's just fine ... Am I making a mistake or does this not work inherently? Thanks, Joh params <- new( "GOHyperGParams", geneIds = BunchOfIPIIds, universeGeneIds = BiggerBunchOfIPIIds, annotation = IPI.MOUSE.3.37.20080509.db, ontology = "BP", pvalueCutoff = 1.0, testDirection = "over" ) HGT <- hyperGTest(params)

Hi, I suspect that the issue is one of what IDs you are supplying and what it is expecting. The error message points to, getUniverseHelper and you can see the source code from within R, via Category:::getUniverseHelper and you can do something like: debug(Category:::getUniverseHelper) to have execution stop when you enter this function. At that point, you can query to see what probes is, what datPkg is and what the entrezIDs are. I would then check to see what the value of univ is (the first command), and see how that compares with the supplied entrezIds - my guess is that these are not using the same IDs, and hence there are no matches :-(, but that might give you a hint as to how to fix things, for your case, best wishes Robert ps things have changed a bit, and will change more soon, in devel, but I doubt those changes will relate to your problem - but as you give no version information.. Johannes Graumann wrote: > I asked this a while ago, but didn't get any further ... > > I built an annotation package for a mouse IPI database using "AnnotationDbi" > (IPI.MOUSE.3.37.20080509.db) and am now putting it to use with "hyperGTests" > from "GOstats". > The annotation package mapps all IPI IDs as "probes" to the relevant > annotation data and I thought it should be possible to hand "geneIds" and > universeGeneIds in the form of probe names (here IPI IDs) to the hyperGTest > function. If I do so I always get the error: > # Error in getUniverseHelper(probes, datPkg, entrezIds) : > # No Entrez Gene ids left in universe > If I use the annotation package to pre-convert the probes (IPI IDs) into > entrez-IDs everything's just fine ... Am I making a mistake or does this > not work inherently? > > Thanks, Joh > > params <- new( > "GOHyperGParams", > geneIds = BunchOfIPIIds, > universeGeneIds = BiggerBunchOfIPIIds, > annotation = IPI.MOUSE.3.37.20080509.db, > ontology = "BP", > pvalueCutoff = 1.0, > testDirection = "over" > ) > HGT <- hyperGTest(params) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org