[BioC] ReadAffy() for customized Affy chips

[Li,Qinghong,ST.LOUIS,Molecular Biology]

Thanks Jim.

Thanks for providing the helpful information. I tried both make.cdf.package and makecdfenv. I was able to make the env successfully.

But for some reason, the package made from make.cdf.package didn't work -- I was not able to install it. I used  "Install package(s) from local .zip files" dropdown manual (I zipped the package I made), but I got this message: 

> utils:::menuInstallLocal()
Error in gzfile(file, "r") : unable to open connection
In addition: Warning messages:
1: error -1 in extracting from zip file 
2: cannot open compressed file 'cxxxx500001cdf/DESCRIPTION' 

Not sure what was going on with the package I made. But at least one of the methods works. 

Johnny


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of James W.
MacDonald
Sent: Thursday, November 10, 2005 3:08 PM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] ReadAffy() for customized Affy chips


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]]
> 
> _______________________________________________ Bioconductor mailing
> list Bioconductor at stat.math.ethz.ch 
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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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