[BioC] Help with annotation packages

[sdurinck at ebi.ac.uk]

Hi Amy,

> My confusion is really over which package to use:
>
> I understand that Biomart can handle single queries or queries for a small
> list of (e.g.) DE genes, but not the entire probe set.  Is that right?


This is not true.  You can use it for long lists as well, the maximum I
tried is to annotate about 20.000 ids at once, even longer lists are
possible.

> Also, I note that other list users with queries relating to Biomart have
> been directed to use the devel version.  I think this doesn't work with R
> 2.2.1?

This is correct, it is recommended to use the latest devel version of
biomaRt and you'll need R-2.3.0 for this of which you can find a Windows
version here:

http://cran.r-project.org/bin/windows/base/rdevel.html

Cheers,
Steffen