[BioC] ReadAffy() for customized Affy chips

[James W. MacDonald]

Li,Qinghong,ST.LOUIS,Molecular Biology wrote:
> Dear BioC,
> 
> We have our own customized Affy chip. I got my CEL files and related
> CDF file. Based on the book "The Analysis of Gene Expression Data" by
> editors Parmigiani et al., I put all the files under the working dir,
> and evoke the function ReadAffy(). After that, I tried to use hist()
> or boxplot(), I got the following error message:
> 
> Error in getCdfInfo(object) : Could not obtain CDF environment,
> problems encountered: Specified environment does not contain
> Cxxxxx500001 Library - package cxxxxx500001cdf not installed Data for
> package affy did not contain cxxxx500001cdf
> 
> Also tried read.celfile() and read.cdffile(), but those methods were
> not recognized. I guess, over the time, the package Affy has been
> modified.
> 
> Now, my question is: how am I going to read in the CDF file? Since it
> is our own chip, I have nether package cxxxx500001cdf nor package
> Cxxxx50001probe. Should I create my own packages? If so, how to do
> that?

See ?make.cdf.package and ?make.cdf.env in the makecdfenv package as 
well as ?makeProbePackage in matchprobes package.

Also, note that any package you create has to be installed. If you make 
an env, you don't have to install that, but it will only persist in the 
existing workspace so is not as nice as a package. Note too that if you 
make a cdfenv (rather than package), you need to name it Cxxxxx500001 or 
the affy package will not find it.

To install packages, see 5.1 Installing packages in 'R Installation and 
Administration', which can be accessed on the start page of the HTML 
help (invoked by help.start()).

HTH,

Jim


> 
> 
> Thanks a million! Johnny
> 
> [[alternative HTML version deleted]]
> 
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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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