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List:       bioconductor
Subject:    Re: [BioC] Can I use Bioconductor to parse *.chp (Affymetrix) files?
From:       "James W. MacDonald" <jmacdon () med ! umich ! edu>
Date:       2010-08-30 16:34:21
Message-ID: 4C7BDD8D.9000209 () med ! umich ! edu
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Hi Anton,

On 8/30/2010 6:25 AM, Anton Kratz wrote:
> Hi,
> 
> I have a bunch of Affymetrix *.chp files in binary format. I do not have
> access to Affymetrix software for working with this and I want to do
> subsequent analysis of this data with my own scripts anyway.
> 
> Can I use Bioconductor to convert such binary *.chp files into
> human-readable cleartext (f.e. tab-delimited table)? Or otherwise parse
> them?
> 
> My goal would be a file with genes (not probes) and their expression values.
> As I understand it, normalization, summarization etc has already been done
> and is somewhere in the *.chp files, but I don't see a way to get the data.
> 
> I figured out that Bioconductor let's me work with *.cel files using the
> affy package, but what about *.chp?!

Yup. See readChp() in the affxparser package.

Best,

Jim


> 
> Thanks.
> 
> Anton
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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