[BioC] justRMA/GCRMA and alternative cdfs

[James MacDonald]

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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