[BioC] How map probeset_id to gene_symbols or other annotation information?

[Peng Yu]

On Sun, Aug 9, 2009 at 7:01 AM, Sean Davis<seandavi at gmail.com> wrote:
>
>
> On Sat, Aug 8, 2009 at 6:31 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
>>
>> Hi,
>>
>> I have run the following 'run.R' script, which generated the file
>> 'gene.txt'. My question is how to map the probeset_ids to the gene
>> names or other information that is available in
>>
>> http://www.affymetrix.com/analysis/downloads/na29/wtgene/MoGene-1_0-st-v1.na29.mm9.probeset.csv.zip?
>> What package I should use to read the '.csv' file?
>
> Hi, Peng.  You will probably want to do some reading before posting.  There
> is an entire manual on input/output with R available from CRAN that you
> should read.
>
> http://watson.nci.nih.gov/cran_mirror/manuals.html

I don't have time to read all the manual. Which manual should I in
particular focus on? "R Data Import/Export"? Would you please point to
me which section is the most important for my task?

> Let us know if you have questions about reading .csv files after you have
> read that manual.
>
> As a recommended alternative, have a look at the package:
>
> http://bioconductor.org/packages/2.4/data/annotation/html/mogene10stprobeset.db.html

This package only has a reference, which is hard for a newbie to
figure out how to use it. I will appreciate you if you could provide
some examples on how to annotate my data.

Regards,
Peng