Hi, I was wondering if it exists an annotation package for Affy 133plus2 reporting the number of synonymous & non synonymous changes for the genes on the array. If it does not exist does anybody has a good suggestion about how to retrive this information from databases ? Marco

Hi Marco, You can do this with the biomaRt package (use the devel version, >= 1.9.21) , here's how: library(biomaRt) mart=useMart("ensembl", dataset="hsapiens_gene_ensembl") getBM(attributes=c("ensembl_gene_id","ensembl_transcript_id","synonymo us_snp_count","non_synonymous_snp_count"), filters="affy_hg_u133_plus_2", values=c("201746_at","231640_at"), mart=mart) it will give: ensembl_gene_id ensembl_transcript_id synonymous_snp_count non_synonymous_snp_count 1 ENSG00000141510 ENST00000269305 5 20 2 ENSG00000133703 ENST00000256078 1 1 3 ENSG00000133703 ENST00000311936 1 1 Unfortunately you won't be able to get the affy id in the output but you can use biomaRt to map the Ensembl ids in the output back to the afffy ids. Cheers, Steffen marco zucchelli wrote: > Hi, > > I was wondering if it exists an annotation package for Affy 133plus2 > reporting the number of synonymous & non synonymous changes for the > genes on the array. > > If it does not exist does anybody has a good suggestion about how to > retrive this information from databases ? > > > Marco > > _______________________________________________ > 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 >