I am trying to normalize 60 rat arrays, Affy 230.2 with the custom cdfs available from MBNI. RMA blows up due to memory limitations so I tried to hack justRMA to take the custom cdfs without success. Is this possible? Thanks, Mark W. Kimpel MD Department of Psychiatry Indiana University School of Medicine Biotechnology, Research, & Training Center 1345 W. 16th Street Indianapolis, IN 46202

Kimpel, Mark William wrote: > I am trying to normalize 60 rat arrays, Affy 230.2 with the custom cdfs > available from MBNI. RMA blows up due to memory limitations so I tried > to hack justRMA to take the custom cdfs without success. Is this > possible? Yep. Two ways. First, to just hack things to work one time you can type just.rma at an R prompt, copy the code, and make the following change: headdetails <- .Call("ReadHeader", filenames[[1]], compress, PACKAGE = "affy") dim.intensity <- headdetails[[2]] cdfname <- "MBNIcdfname" ## this is the changed line ## tmp <- new("AffyBatch", cdfName = cdfname, annotation = cleancdfname(cdfname, addcdf = FALSE)) pmIndex <- pmindex(tmp) you will also need to copy read.probematrix and make a similar change: headdetails <- .Call("ReadHeader", filenames[[1]], compress, PACKAGE = "affy") dim.intensity <- headdetails[[2]] ref.cdfName <- headdetails[[1]] Data <- new("AffyBatch", cdfName = ref.cdfName, annotation = cleancdfname(ref.cdfName, addcdf = FALSE)) Data at cdfName <- "MBNIcdfname" ## this is the changed line ## Then either paste or source() the hacked code back into your R session and proceed as normal. The non-hackish way to change things would be to add a cdfName variable to the calls for justRMA(), just.rma() and read.probematrix() so one could be specified at the outset: eset <- justRMA(cdfName = "MBNIcdfname") I will look into adding this to the devel version. HTH, Jim > > Thanks, > > Mark W. Kimpel MD > > Department of Psychiatry > > Indiana University School of Medicine > > Biotechnology, Research, & Training Center > > 1345 W. 16th Street > > Indianapolis, IN 46202 > > _______________________________________________ > 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