[BioC] GOstats : Error in getUniverseHelper - No Entrez Gene ids left in universe

Heidi Dvinge heidi at ebi.ac.uk
Thu Aug 6 00:04:25 CEST 2009


Hi Ben,

your IDs are RefSeq, and org.Mm.eg.db expects Entrez Gene (the "eg" part
of the package name). Try converting them with "org.Mm.egREFSEQ2EG" first.

Cheers
\Heidi

> Hi,
>
> I am getting this error when I run hyperGTest from GOstats. Any idea on
> what is going wrong would be appreciated ?
>
> R version 2.8.1 (2008-12-22)
> GOstats  1.7.4
> I am also attaching the files genefile/universe.txt
>
> write.table(ori$Accession, "universe.txt", sep = "\t",
> quote=FALSE,row.names=FALSE,col.names=FALSE)
>
> geneFile  <- "genefile.txt"
> uniFile   <- "universe.txt"
>
> universe  <- scan(uniFile, what="character")
> genelist  <- scan(geneFile, what="character")
>
> pcut    <- 0.05
> catSize <- 5
>
>
> params    <- new("GOHyperGParams", geneIds=genelist,
> universeGeneIds=universe,
>                annotation="org.Mm.eg", ontology="BP", pvalueCutoff=pcut,
>                conditional=FALSE, testDirection="over")
>
>
> results <- hyperGTest(params)
> Error in getUniverseHelper(probes, datPkg, entrezIds) :
>    No Entrez Gene ids left in universe
>
>
>
>
> Thanks,
>
> Ben
>
>
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