[BioC] justRMA with custom cdfs

James W. MacDonald jmacdon at med.umich.edu
Mon Jan 23 16:13:13 CET 2006

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 = 
         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.



> 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

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