I'm trying to convert ensembl gene ids to mgi ids. I know that I can do this in biomart, but I recently noticed there are a number of mouse annotation packages. I was just wondering what is the best/easiest way to do this?
How you define 'best' is sort of personal. I personally prefer to use the annotation packages directly, but biomaRt is a perfectly good way to go as well. If you want to use the annotation packages, you can use either select() or mapIds(). The difference being that mapIds() will by default silently choose one result for any one-to-many mappings whereas select() will not.