[BioC] GOstats After Running Lumi

[Paul Leo]

Other than :

htmlReport(hgOver,file="GO_summary.html")
OR
summary(hgOver)

Perhaps no significant GO's at pvalueCutoff= 0.01

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Shawn
Westaway
Sent: Friday, 4 May 2007 11:30 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] GOstats After Running Lumi

Using Lumi on Illumina Mouse-Ref6 chip microarray data. I tried to use
GOstats to generate a nice table like the one shown in lumi.pdf using
the following script

> if (require(GOstats) & require(lumiMouseV1)) {
sigLL <- unique(unlist(mget(sigGene, env=lumiMouseV1ENTREZID,
ifnotfound=NA)))
sigLL <- as.character(sigLL[!is.na(sigLL)])
params <- new("GOHyperGParams",
geneIds= sigLL,
annotation="lumiMouseV1",
ontology="BP",
pvalueCutoff= 0.01,
conditional=FALSE,
testDirection="over")
hgOver <- hyperGTest(params)
gGhyp.pv <- pvalues(hgOver)
sigGO.ID <- names(gGhyp.pv[gGhyp.pv < 0.001])
sigGO.Term <- getGOTerm(sigGO.ID)[["BP"]]
}

The script does not seem to output anything. Is there a command missing
to generate the data?
Thanks,
Shawn

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