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

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. Best, Jim > > > regards > > > Anthony > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- 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