[BioC] Help with HyperGTest

Marc Carlson mcarlson at fhcrc.org
Tue Nov 10 18:39:23 CET 2009

Hi Yue,

It's a good idea to always give us the output of sessionInfo() when you
post, but I can tell you that with this error, the problem is usually
caused by the input IDs.  If you are using the org.EcK12.eg.db then  you
must use IDs that are Entrez Gene IDs.  What is the output from
head(targetids) and head(ecoliids)? 


Yue, Chen - BMD wrote:
> Dear All,
> I hope to get some help on the hyperGTest in GOstats. I want to do an GO enrichment anlaysis on a set of E. coli K12 genes (substr DH10B). I attached the target id file, partial ecoli id file (as universeGeneIds) and sessionInfo to the email. The following is my commands and error. It seems that my gene id is not found in the annotation package but I don't know how to find out what gene ids are included in the package. I used "org.EcK12.eg.db" package which uses Entrez ids and my R version is 2.9.2 on WinXP. Should I use a different annotation package? Thank you very much!
>> targettable <- read.table("D:/RProjects/targetids.txt")
>> ecolitable <- read.table("D:/RProjects/ecoliids.txt")
>> targetids <- unique(targettable[,1])
>> ecoliids <- unique(ecolitable[,1])
>> params = new("GOHyperGParams", geneIds=targetids, universeGeneIds=ecoliids, annotation="org.EcK12.eg.db", ontology="BP", pvalueCutoff=0.01, conditional=FALSE, testDirection="over")
>> BPoverTest = hyperGTest(params)
> Error in getUniverseHelper(probes, datPkg, entrezIds) : 
>   After filtering, there are no valid IDs that can be used as the Gene universe.
>   Check input values to confirm they are the same type as the central ID used by your annotation package.
>   For chip packages, this will still mean the central GENE identifier used by the package (NOT the probe IDs).
> Regards,
> Yue
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