On Sun, Aug 9, 2009 at 11:53 AM, Peng Yu <pengyu.ut@gmail.com> wrote:

> On Sun, Aug 9, 2009 at 7:01 AM, Sean Davis<seandavi@gmail.com> wrote:
> >
> >
> > On Sat, Aug 8, 2009 at 6:31 PM, Peng Yu <pengyu.ut@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?


Hi, Peng.

I don't mean to sound rude, but everyone on this list is quite busy.  You
will need to make time to do some of your own research, unfortunately.  As
an exercise and an answer to your question, check out the Table of Contents
of the R Data Import/Export.  If there is still a question about what
section is most appropriate, feel free to post back to the list the code you
have tried, any error messages, and the output of sessionInfo().  And, yes,
you will benefit from at least skimming the entire manual--you will learn
quite a bit.


>
> > 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.
>

Good point.  The annotation packages are generally based on information
given here:

http://bioconductor.org/packages/release/bioc/html/AnnotationDbi.html

While the examples in the vignette use a different chip type, it should be
possible to extrapolate to the mogene arrays.

Sean

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