I have been using biomaRt to convert Affy probes to HUGO gene names. Using the same set of probes, I got a different number of genes last month using the previous version of biomaRt, and I get slightly less genes now with the current version of biomaRt. Why has this difference occurred? I have some data from the previous mapping, and I want all my data to be consistent. Is there a way to access (install) the previous version of bioMart (the one I used on March 8th)?
Here is my conversion code:
entrezgeneids = gsub('_at', '', row.names(expr)) organism = 'hsapiens_gene_ensembl' ensemble = useMart('ensembl'); hsp = useDataset(mart=ensemble,dataset=organism); ids = getBM(filters='entrezgene', attributes=c('entrezgene','hgnc_symbol'), values=entrezgeneids, mart=hsp)
Thanks!
Glad it helped. And with your addition this makes a much more complete answer!