[BioC] Affymetrix Mouse Promoter array / pdInfoBuilder

zacher at lmb.uni-muenchen.de zacher at lmb.uni-muenchen.de
Mon Oct 12 19:16:21 CEST 2009

Dear Hans-Ulrich,

The package affxparser contains functions to read and write bpmap files. The function readBpmap returns a list which also contains the probe sequences.
A remapping can e.g. be done with MUMmer or the bioconductor package
Biostrings. Here is a short workflow, that you could do with Biostrings.

Ringo and Starr are packages for the analysis of ChIP-chip experiments.
Starr provides functions for Affymetrix, Ringo for Nimblegen and Agilent but 
they use the same data structures.
First you must convert the bpmap file with Starr to a pos file, which is
Nimblegen file format. The package Ringo contains R and perl scripts for 
mapping the sequences with Biostrings (or other programs like MUMmer). 
You can find them in the /inst/scripts folder.
The remapping is saved as a pos file. Then use posToProbeAnno to generate
a probeAnno object (Ringo). After that, use Starr to read the cel files to an 
ExpressionSet and start your analysis.
Best regards


Hans-Ulrich Klein <h.klein at uni-muenster.de> schrieb :

> Hi All,
> I have ChIP-chip data based on the Affymetrix Mouse Promoter platform. I 
> built a &quot;pd.mm.prompr.v02&quot; 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 
> &quot;pd.mm.prompr.v02&quot; package. The pdInfoBuilder takes a
> &quot;bpmap&quot; file that 
> can be downloaded from affymetrix.com. The newest file has coordinates 
> for the &quot;NCBI36&quot; mouse assembly and thus is outdated.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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