[BioC] Help with HyperGTest
Yue, Chen - BMD
yuechen at bsd.uchicago.edu
Sat Nov 7 18:45:38 CET 2009
I'm new to Bioconductor, so I apologize if my problem is too naive. I want to do an GO enrichment anlaysis on a set of E. coli K12 genes (substr DH10B). I attached the target id file and ecoli id file (as universeGeneIds) 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. Can someone help me find out what is wrong? 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).
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