[BioC] GOstats After Running Lumi

[James W. MacDonald]

Hi Shawn,

Shawn Westaway wrote:
> 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?

First off, you are missing the universeGeneIds. I don't know what 
hyperGTest will do in that situation, but it can't be as good as 
actually specifying one.

Second, I don't think you need to do all that stuff after hyperGTest. A 
simple summary(hgOver) should suffice, and if you want output 
htmlReport(hgOver, file="My BP GO terms.html") will make an HTML page.

Best,

Jim


> Thanks,
> Shawn
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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