[BioC] Affymetrix HT HG-U133+ PM Array Plate annotation data

[James W. MacDonald]

Marc Carlson 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.

Actually we _do_ have an annotation package for that chip. It's the 
hgu133plus2.db package.

The only difference between the two chips is the fact that they dropped 
the MM probes, and reduced the number of PM probes in some of the 
probesets.

Oh yeah, and they added a _PM_ to the probeset ID, so there will be some 
name mangling required to use the hgu133plus2.db package.

Best,

Jim




> 
> 
>   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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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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