[BioC] Using BrainArray mappings with oligo package

Steve Piccolo stephen.piccolo at hsc.utah.edu
Fri May 18 22:09:08 CEST 2012

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?


Stephen Piccolo, Ph.D.
Postdoctoral Researcher

  Department of Pharmacology and Toxicology, University of Utah
  Computational Biomedicine Section, School of Medicine, Boston University

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