Hi Suman Better posting this to: bioconductor at stat.math.ethz.ch See www.bioconductor.org for mailing list details. best iain --- On Tue, 28/6/11, suman pal <jigassa at="" yahoo.com=""> wrote: > From: suman pal <jigassa at="" yahoo.com=""> > Subject: [R] help required for GO Annotation problem > To: r-help at r-project.org > Date: Tuesday, 28 June, 2011, 10:34 > Hello, > I basically want to use R-help, and post some problems > which I am facing. The Ref is a well known Genome Biology > paper "Bioconductor: open software development for > computational?biology and bioinformatics" by?Robert C > Gentleman et al., 2004. Generating Heatmaps till Fig2 is > working so I think esetSel is not the problem.. > However, for generating the Figure 3, for GO annotations > the following command is not working: > > ll <- mget(geneNames(esetSel),hgu95av2LOCUSID) > ?? > #it is displaying error messages ?Error in > mget(geneNames(esetSel), hgu95av2LOCUSID) : object > 'hgu95av2LOCUSID' not foundand also geneNames not found try > featureNames instead > Hence I cant proceed to the next set of commands provided > in the paper which are as follows: > > ll <- unique(unlist(ll))> mf <- > as.data.frame(GOHyperG(ll))[, 1:3]> mf <- mf[mf$pvalue > < 0.01, ] > sincerelySumanCCMB Hyderabad. > > ??? [[alternative HTML version deleted]] > > > -----Inline Attachment Follows----- > > ______________________________________________ > R-help at r-project.org > mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- guide.html > and provide commented, minimal, self-contained, > reproducible code. >