3.8 years ago by
There are at least two other ways you could approach this. First, if you are using limma to do the analysis (and you probably should be doing that), then when you read the data into an RGList, the 'genes' list item will contain accession numbers that you can use to map to Ensembl using the org.Mm.eg.db package. Something like
dat <- read.maimages(<filenames go here>, source = "agilent.median")
gns <- dat$genes
## there should be a column called 'Systematic name' or something like that, which contains the accession numbers. You can then map using
ensgene <- mapIds(org.Mm.eg.db, as.character(gns[,<correct column number goes here>]), "ENSEMBL","ACCNUM")
An alternative would be to get the data from GEO. You could use GEOquery to get those data, or just download by hand and parse out the column containing the Ensembl IDs.