[BioC] Using BrainArray mappings with oligo package

Benilton Carvalho beniltoncarvalho at gmail.com
Tue May 22 22:02:44 CEST 2012

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.


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
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