[BioC] Affymetrix Mouse Promoter array / pdInfoBuilder

Benilton Carvalho bcarvalh at jhsph.edu
Mon Oct 12 17:03:04 CEST 2009

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  

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  

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

With best wishes,


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 for the "NCBI36" mouse assembly and thus is outdated.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
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list