[BioC] symbol annotation using probes2tableBM

[James W. MacDonald]

Hi Mayte,

This is a bug that has been fixed in the devel version of affycoretools. 
The problem comes from the fact that the 'symbol' descriptor is 
different in the human vs mouse (hgnc_symbol vs markersymbol).

Best,

Jim



Mayte Suarez-Farinas wrote:
> Hi,
> 
> I am Trying to get mouse4302 affy ID annotation from BioMart using  
> probes2tableBM function:
> 
> probes2tableBM(fileset,  
> probids=ids,filename='test',species="mmusculus",  
> ann.source="affy_mouse430_2", links=linksBM()[c(1:3,5)],  
> otherann=annBM()[1:2], affyid=TRUE, express=FALSE)
> 
> but the column Symbol do not appear in the output.
> 
> If I do the following:
> mart=useMart("ensembl", dataset="mmusculus_gene_ensembl")
> Checking attributes and filters ... ok
>  > otherann <- annBM(mart)
>  > otherann
> [1] "Description" "GO"          "GOID"        "Chromosome"  "ChromLoc"
> 
> 
> so, symbol do not appear in theannBM output either.
> but if I get the BM annotation directly, the symbol is available:
> 
> getBM(c("affy_mouse430_2","entrezgene","markersymbol","refseq_dna"),  
> filters="affy_mouse430_2", values="1442021_at", mart=mart)
>    affy_mouse430_2 entrezgene markersymbol refseq_dna
> 1      1442021_at      14680         Gnal  NM_177137
> 
> 
> so, I guess the problem could be in AnnB..
> 
> 
> 
> 
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> 
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