Dear List: I've been using the oligo package for reading and normalizing CEL files. It's a very useful package! Now I'm hoping to map individual probes to genes using the BrainArray mappings (http://brainarray.mbni.med.umich.edu). From reading the documentation, it sounds like I will need to use the pdInfoBuilder package to construct a new annotation package from the BrainArray CDF files. But I want to be able to do this for basically all array versions and for each annotation source (e.g. Entrez Gene, Ensembl, etc.). I guess I could contact the BrainArray folks and see if they'd be willing to provide this, or I could build these packages on the fly. Is there any alternative? Am I missing something that is already out there? Regards, Stephen ---------------------------------------------------------------------- ----- ---------------------------- Stephen Piccolo, Ph.D. Postdoctoral Researcher Affiliations: Department of Pharmacology and Toxicology, University of Utah Computational Biomedicine Section, School of Medicine, Boston University

Hi Steve, sorry for the late reply... There isn't anything implemented in oligo/pdInfoBuilder that allows one to create the required objects on the fly. If you had at least the PGFs (ideally PGFs, MPS, transcript/probeset files) associated with the alternative annotation, then it would be as simple as creating a regular pdInfoBuilder package. Affymetrix themselves do not support CDFs for WT arrays and I don't build annotation packages using unsupported resources. benilton On 18 May 2012 21:09, Steve Piccolo <stephen.piccolo at="" hsc.utah.edu=""> wrote: > Dear List: > > I've been using the oligo package for reading and normalizing CEL files. > It's a very useful package! > > Now I'm hoping to map individual probes to genes using the BrainArray > mappings (http://brainarray.mbni.med.umich.edu). From reading the > documentation, it sounds like I will need to use the pdInfoBuilder package > to construct a new annotation package from the BrainArray CDF files. But I > want to be able to do this for basically all array versions and for each > annotation source (e.g. Entrez Gene, Ensembl, etc.). I guess I could > contact the BrainArray folks and see if they'd be willing to provide this, > or I could build these packages on the fly. Is there any alternative? Am I > missing something that is already out there? > > Regards, > Stephen > > -------------------------------------------------------------------- ------- > ---------------------------- > Stephen Piccolo, Ph.D. > Postdoctoral Researcher > > Affiliations: > ?Department of Pharmacology and Toxicology, University of Utah > ?Computational Biomedicine Section, School of Medicine, Boston University > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor