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!

Thanks, this helped a lot. Actually, the version of the ensembl I used earlier was not available in the archived BioMarts, so I had to leave archive = FALSE and to specify the url of the archived BioMart, as below:

ensembl=useMart(host="dec2014.archive.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")

Probably the new biomaRt version is using an updated Ensembl database. You can choose to use an older database by means of archives. This only requires that you know the version being used when you analyzed your data. From the biomaRt vignette:

library(biomaRt)
listMarts(archive = TRUE)
# use ensembl version 46.
ensembl <- useMart("ensembl_mart_46", dataset = "hsapiens_gene_ensembl", archive = TRUE)