[BioC] justRMA/GCRMA and alternative cdfs

[James MacDonald]

Just an update - ReadAffy() and friends will now also accept a cdfname argument. 

The resulting exprSet will now contain the correct cdf name in the annotation slot, which wasn't true if one simply replaced the contents of the cdfName slot in an AffyBatch.

As usual, the changes are in the subversion repository and will propagate to the devel repository within a few days.

Best,

Jim



James MacDonald wrote:
> For those who are interested, I just committed changes to both justRMA() and justGCRMA() that will allow the use of alternative cdfs (and probe packages in the case of justGCRMA()).
> 
> I added a 'cdfname' argument to both functions, so as an example if you have an alternative cdf called "mm430mmentrezg6cdf", you would use
> 
> justRMA(cdfname = "mm430mmentrezg6")
> 
> Note that the argument is the package name *minus* the 'cdf' at the end. This is for consistency with rma() and gcrma().
> 
> Also note that this change does not affect the normal functionality - justRMA() and justGCRMA() without a cdfname argument will use the normal Affy-based cdf and probe packages.
> 
> These changes are in the devel versions of the affy and gcrma packages, and may take a couple of days to propagate to the download repository.
> 
> Best,
> 
> Jim
> 
> 
> 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> 
> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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