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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