[BioC] [R] help required for GO Annotation problem

[Iain Gallagher]

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.
> 
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> 
> 
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