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 <- getGOTermsigGO.ID)[["BP"]] } The script does not seem to output anything. Is there a command missing to generate the data? Thanks, Shawn

"James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > 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. If left unspecified, all genes probed on the chip are used as the universe. I fully agree that this is in most cases a suboptimal choice. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

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 <- getGOTermsigGO.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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

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@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 <- getGOTermsigGO.ID)[["BP"]] } The script does not seem to output anything. Is there a command missing to generate the data? Thanks, Shawn _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

I am sorry, Seth and James, but I did not understand the universeGeneIds command. Is this something I am supposed to generate from limma? Shawn >>> "Seth Falcon" <sfalcon at="" fhcrc.org=""> - 5/3/07 8:22 PM >>> "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > 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. If left unspecified, all genes probed on the chip are used as the universe. I fully agree that this is in most cases a suboptimal choice. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor