[BioC] justRMA and custom CDF

James W. MacDonald jmacdon at med.umich.edu
Fri Dec 23 14:55:04 CET 2005

Anthony Bosco wrote:
> Hi ,
> I would like to analyse a large Affymetrix dataset with justRMA 
> function and a custom CDF.
> Is this possible?

Yes it is possible, but you will have to convert the cdf into either a 
cdfenv or a cdf package first. See ?make.cdf.env and ?make.cdf.package 
in the matchprobes package.

One caveat; if you make the package you should not specify a name, as 
make.cdf.package will name it correctly for you. However, if you are 
making an environment, you need to specify a name which should be the 
name of the cdf file minus the .cdf portion. Note that the name is 
case-sensitive. If you mis-name the cdfenv, then the affy package will 
not be able to find it.



> regards
> Anthony
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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