[BioC] GOstats suggestion

[Dick Beyer]

Hi Jo,

I looked at all the responses to your GOstats question and I'm wondering why no one is mentioning using the topGO package.  It seems to do what you want, that is, you define your universe however you want.  You don't have to use affy annotation.

Cheers,
Dick

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Richard P. Beyer, Ph.D.	University of Washington
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Message: 6
Date: Mon, 4 Jun 2007 16:56:42 +0200
From: "Johannes Rainer" <johannes.rainer at tcri.at>
Subject: Re: [BioC] GOstats suggestion
To: "Joern Toedling" <toedling at ebi.ac.uk>
Cc: bioconductor at stat.math.ethz.ch
Message-ID:
 	<ae8a85340706040756w2c55651i23280947ac908902 at mail.gmail.com>
Content-Type: text/plain

thanks for your suggestion, this would be a solution,
but as far as i understand the functions from the GOstats and Category
packages map each time the hyperGTest function is called the submitted ids
to GO terms using the annotation packages (i.e. hgu133plus2 annotation
packages). actually the mapping is performed in the getGoToEntrezMap
function (Category package), and this function maps EntrezGene IDs to GO
terms by first mapping affy IDs to GO terms and then affy IDs to EntrezGene
IDs.
when i submit the EntrezGene IDs of the selected genes and those of the gene
universe, i would not need the information from the annotation packages that
map affy ids to entrezgene ids and affy ids to GO terms. the mapping between
GO terms and EntrezGene IDs can be performed using the GO package
i.e.

     GOLL <- as.list(get("GOALLENTREZID",mode="environment"))
     GOLL <- GOLL[!is.na(GOLL)] # just removing all the GO ids that are not
mapped to any EntrezGene ID
     PresentGO <- sapply(GOLL,function(z){
         if(is.na(z) || length(z)==0)
             return(FALSE)
         any(x %in% z)            # x are EntrezGene IDs, either from the
gene universe or the selected ones
         }
     )

    GOLL <- GOLL[PresentGO]

GOLL is than a list of all GO terms for the EntrezGene IDs specified with x
(containing all ontologies, MF, CC and BP)

i think using the GO/EntrezGene mapping from GO package would not restric
the GO analysis to platforms/micro arrays where annotation packages exist...

sincerely, jo


On 6/4/07, Joern Toedling <toedling at ebi.ac.uk> wrote:
>
> Hello Johannes,
>
> you can use BioConductor's "AnnBuilder" package to produce a custom
> annotation package for your own selection of EntrezGeneIDs and then use
> GOstats with this custom annotation package. This may be more efficient
> than mapping EntrezGeneIDs to GO nodes each time you run GOstats. Having
> said that, I have to admit that it took some time to get AnnBuilder
> running due to its dependencies.
>
> Best regards,
> Joern
>
> Johannes Rainer wrote:
> > dear Seth, dear Bioconductor members,
> >
> > as far as i understand you are using the annotation package defined with
> the
> > "annotation" parameter (GOHyperGParams) to map the submitted
> EntrezGeneIDs
> > to the GO terms. this works fine for Affymetrix arrays with available
> > annotation packages, but we are for example also using Exon arrays and
> are
> > annotating the probes on our own. my suggestion is to support also the
> > mapping from EntrezGene IDs to GO terms using the GO package. this would
> > allow GO analyses for all microarray platforms, not just Affmetrix
> arrays
> > with available annotation packages.
> >
> >
> > sincerely, jo
> >
> >
> >
>
>


-- 
Johannes Rainer, Msc
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Austria
Tel.: +43 512 570485 33
Email: johannes.rainer at tcri.at
           johannes.rainer at tugraz.at

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