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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.. > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor