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

[Marc Carlson]

Hi Benoit,

One more thing that might help you is the new AnnotationDbi vignette
which should demonstrate how you could convert those refseq IDs into
entrez gene IDs.  The org.Mm.egREFSEQ mapping in the org.Mm.eg.db
package should have the information that you need.  You can read the
very latest version of this document here:

http://www.bioconductor.org/packages/devel/bioc/vignettes/AnnotationDbi/inst/doc/AnnotationDbi.pdf


  Marc



Marc Carlson wrote:
> 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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