[BioC] Affymetrix Mouse Promoter array / pdInfoBuilder

Hans-Ulrich Klein h.klein at uni-muenster.de
Mon Oct 12 16:09:43 CEST 2009

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for the "NCBI36" mouse assembly and thus is outdated.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.


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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