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 The newest file has coordinates for the "NCBI36" mouse assembly and thus is outdated.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 M?nster Domagkstrasse 9 48149 M?nster, Germany Tel.: +49 (0)251 83-58405

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 for the "NCBI36" mouse assembly and thus is outdated.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 M?nster > Domagkstrasse 9 > 48149 M?nster, 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

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 Benedikt 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 "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 M?nster > Domagkstrasse 9 > 48149 M?nster, 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