[R] help required for GO Annotation problem

[James W. MacDonald]

Hi Suman,

On 6/28/2011 10:02 AM, David Winsemius wrote:
>
> 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

As David notes, this question is better asked on the BioC listserv. And 
it is really old code. The LOCUSID object has been deprecated for a long 
time now, replaced by ENTREZID, and as the warning notes, geneNames() 
has been deprecated in favor of featureNames.

So try

ll <- mget(featureNames(esetSel), hgu95av2ENTREZID)

also GOHyperG() is gone as well, replaced by S4 methods that might be a 
bit less easy to figure out. I don't have the book you are working 
through, but you would be better served if you were to use the vignettes 
that come with the packages you are using instead (or at least as a way 
to get updated examples of how to use the package).

Anyway, please direct all future questions about BioC packages to the 
BioC listserv.

Best,

Jim


>
> 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.
>
>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> 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.
>
> David Winsemius, MD
> West Hartford, CT
>
> ______________________________________________
> 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.

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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