justRMA/GCRMA and alternative cdfs
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@james-w-macdonald-5106
Last seen 1 hour ago
United States
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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
Microarray Cancer cdf probe affy Microarray Cancer cdf probe affy • 587 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 hour ago
United States
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 > > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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