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

[Marc Carlson]

Hi Benoit,

This error basically means that after filtering, there were no Entrez
Gene IDs left to test on.  Newer versions of this software have more
friendly messages, but there many things that can go wrong with your
inputs that could have caused this.  You might want to look at your
values for genelist and universe and make sure that those are valid
entrez gene IDs etc.

  Marc





Benoit Ballester wrote:
> 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") pmnn
>
> 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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>
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