[BioC] Affymetrix HT HG-U133+ PM Array Plate annotation data
giacomo.tuana at unimib.it
giacomo.tuana at unimib.it
Mon Dec 21 15:38:55 CET 2009
Dear Marc,
I had some trouble with reading external file of probeIDs. I didn't
understand completely the use of system.file( ) command. In the tutorial I
found:
system.file ("extdata", "hcg110_ID",package="AnnotationDbi")
where "extdata" should be my personal tab delimited file for probe ids and
hcg110_ID the source database file?
I'm sorry, but this is the first time I use this commands.
Giacomo
--
Dr. Giacomo Tuana Franguel
Genopolis Consortium
University of Milano-Bicocca
Dept. of Biotechnology and Bioscience/ U4
Piazza della Scienza 4 20126 Milano, Italy
Tel +39 02 6448 3530
Fax +39 02 6448 3550
http://www.genopolis.it
On Fri, 18 Dec 2009 10:00:08 -0800
Marc Carlson <mcarlson at fhcrc.org> wrote:
> Hi Giacomo,
>
> We don't presently have an annotation package for that
>platform. But
> fortunately, we have a solution for you. You can use
>the SQLForge code
> in the AnnotationDbi package to just generate a package
>from an the Affy
> probe to gene mapping files (which you can get from
>their website).
> There is a vignette explaining how to do this here:
>
> http://www.bioconductor.org/packages/2.6/bioc/html/AnnotationDbi.html
>
> Please let me know if you have any trouble.
>
>
> Marc
>
>
>
>
> giacomo.tuana at unimib.it wrote:
>> Dear list,
>> I found only cdf and probe packages for Affymetrix HT
>>HG-U133+ PM Array
>> Plate but there isn't the annotation data package
>>(hthgu133pluspm.db) in
>> Bioc 2.5 and in developing Bioc 2.6. It could be
>>released soon?
>> Thanks!
>> Giacomo Tuana
>> --
>> Dr. Giacomo Tuana Franguel
>> Genopolis Consortium
>> University of Milano-Bicocca
>> Dept. of Biotechnology and Bioscience/ U4
>> Piazza della Scienza 4 20126 Milano, Italy
>> http://www.genopolis.it
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>>
>>
>
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