[R] help required for GO Annotation problem

[David Winsemius]

On Jun 28, 2011, at 5:34 AM, suman pal wrote:

> 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

You seem to be missing a data object. A google search produces this as  
the third hit that suggest you are attempting to run outdate ... well  
it is 7 years old ... code:

http://www.rforge.net/bin/results/compton/2.1/data/annotation/hgu95av2-00check.html

> 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.
>
This would seem a natural question for the BoConductor mailing list...  
after you do a bit more basic searching.


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David Winsemius, MD
West Hartford, CT