[BioC] Affymetrix Mouse Promoter array / pdInfoBuilder

[Benilton Carvalho]

Dear Hans-Ulrich,

Unfortunately, there is no "convenient way" of updating the genomic  
coordinates in the package generated by pdInfoBuilder.

The best option, IMHO, would be generating a new BPMAP with NCBI37  
coordinates. I'm sure Affymetrix provides ways of doing this with  
their SDK, but I don't think the 'affxparser' package provides that  
functionality.

Another possibility is to "manually" modify the SQLite database in the  
pd.mm* package. But that may be dangerous.

Yet another option is to modify pdInfoBuilder itself to allow such  
flexibility.

Regarding the probe sequences, they are in the BPMAP file.

With best wishes,

b

On Oct 12, 2009, at 11:09 AM, Hans-Ulrich Klein wrote:

> Hi All,
>
> I have ChIP-chip data based on the Affymetrix Mouse Promoter  
> platform. I
> built a "pd.mm.prompr.v02" package with the pdInfoBuilder functions  
> and
> read in the CEL files using the oligo package.
> I get stuck with the genome coordinates of the probes provided by my
> "pd.mm.prompr.v02" package. The pdInfoBuilder takes a "bpmap" file  
> that
> can be downloaded from affymetrix.com. The newest file has coordinates
> for the "NCBI36" mouse assembly and thus is outdated. Ensembl (and so
> biomaRt that I want to use for genome annotation) uses NCBI m37  
> assembly.
> Is there a convenient way to integrate newer coordinates or sequences
> provided as text files into the annotation package created by
> pdInfoBuilder? Working with a large data.frame would perhaps be to  
> slow.
> BTW, does anyone know where I can download the probes' sequences? I  
> have
> not found them on affymetrix.com yet.
>
> Best,
> Hans-Ulrich
>
> --
> Hans-Ulrich Klein
> Department of Medical Informatics and Biomathematics
> University of Münster
> Domagkstrasse 9
> 48149 Münster, Germany
> Tel.: +49 (0)251 83-58405
>
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