[BioC] Help with annotation packages

[Amy Mikhail]

Hi Steffen and Jim,

Thanks for the suggestions.  I'll try the whole probeset and a toptable
subset in Biomart and see how I get on.

Cheers,
Amy

> 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
>
>
>
>
>


-------------------------------------------
Amy Mikhail
Research student
University of Aberdeen
Zoology Building
Tillydrone Avenue
Aberdeen AB24 2TZ
Scotland
Email: a.mikhail at abdn.ac.uk
Phone: 00-44-1224-272880 (lab)