[BioC] RMA analysis with new Poplar chip from Affymetrix

[James W. MacDonald]

Cathy Provencher wrote:
> I need some help with bioconductor.
> 
> 
> 
> I have run Poplar chip with the Affymetrix Platform and I want to
> analyze them with RMA using R. However, it seems since it is a new
> microarray chip that the Poplar cdf file is not available on
> bioconductor. I don't know if you are the best person to reach for
> that matter, if yes is it possible to add the Poplar cdf file in the
> library of bioconductor or if you are not the person in charge of
> that can you redirect me to the person in charge of those issues.
> 
> 
> 
> This is the message I got from R.2.2.0

The poplarcdf package is available, but is in the metaData repository 
for release 1.8 (e.g., the devel repository). I think it will work on 
R-2.2.0, so you might just download and install by hand.

http://www.bioconductor.org/packages/data/annotation/1.8/html/poplarcdf.html

HTH,

Jim


> 
> 
> 
> 
>>> rma.set<-justRMA()
> 
> 
> 
> 
>> Error in getCdfInfo(object) : Could not obtain CDF environment,
>> problems encountered:
> 
> 
> 
>> Specified environment does not contain Poplar
> 
> 
> 
>> Library - package poplarcdf not installed
> 
> 
> 
>> Data for package affy did not contain poplarcdf
> 
> 
> 
>> Bioconductor - poplarcdf not available
> 
> 
> 
> 
> 
> 
> Thank your for your help.
> 
> 
> 
> Sincerely,
> 
> 
> 
> Cathy Provencher, M. Sc.
> 
> Microarray Platform Lab,
> 
> McGill University and
> 
> Genome Québec Innovation Centre
> 
> 740, Dr Penfield Avenue, room 6300
> 
> Montreal (Quebec) Canada
> 
> H3A 1A4
> 
> Tel: (514) 398-3311 ext. 00336
> 
> Fax: (514) 398-3763
> 
> 
> 
> 
> 
> 
> [[alternative HTML version deleted]]
> 
> 
> 
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> 
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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