[BioC] GOTERM by itself

[Saurin Jani]

Hi Auer,

I would like to do similar thing with GOTERM as you
are doing at some extent but I would like to build
table like :         (I am using Affy chips here)

GOTERM ,count of ProbeIDS associated with them ,
ProbeIDS itself , SYMBOLS of probe ids

any idea on this ?

Thanks
Saurin





--- Auer Michael <michael.auer at meduniwien.ac.at>
wrote:

> I would like to present the results of GOHyperG in
> the form of a table
> with GO ID, Count, Pvalue and GOTERM. The problem
> lies within the GOTERM
> ,because the output of the enviroment has changed!!!
> 
> 
> 
> I am calling GOHyperG with a series of LOCUS IDS,
> ids1
> 
> ids1MF<-
>
GOHyperG(unique(unlist(ids1)),lib="hgu133a",what="MF")
> 
> Then I am building a matrix with the call. The
> matrix has the columns GO
> ID, Counts and pvalues. But I also want the GOTERM.
> The problem is that
> there is no function which reports the GOTERM by it
> self.
> For example mget("GO:0016407",GOTERM))
> 
> $"GO:0016407"
> GOID = GO:0016407
> GO term = acetyltransferase activity
> Definition for GO term = Catalysis of the transfer
> of an acetyl group to
> an acceptor molecule.
> Ontology = MF
> But I only want the GOTERM
> 
> ids1matrMF<-cbind(names(ids1MF$intCounts),
> as.vector(ids1MF$intCounts), 
> as.vector(ids1MF$pvalues))
> dimnames(ids1matrMF)[[2]]<-c(“GO
> ID”,”Counts”,”pvalues”)
> 
> 
> 
> How can I retrieve only the GOTERM?????
> 
> Thanx
> 
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