[BioC] custom cdf files with just.gcrma

[James W. MacDonald]

D C wrote:
> Is there a way to get just.gcrma to work with a custom cdf file? I
> checked the available documentation and searched the archives but did
> not find anything obvious.

A more recent version of gcrma will allow you to specify an alternative 
cdf in justGCRMA(). From the help file:

Arguments:

      ...: file names separated by comma.

[snip]

  cdfname: Used to specify the name of an alternative cdf package. If
           set to 'NULL', the usual cdf package based on Affymetrix'
           mappings will be used. Note that the name should not include
           the 'cdf' on the end, and that the corresponding probe
           package is also required to be installed. If either package
           is missing an error will result.



Best,

Jim



> 
> I already tried ReadAffy with gcrma and got a memory error:
> 
> data <- ReadAffy() data at cdfName <- "HSFocus_HS_ENTREZG_6" gcrma(data)
>  Thanks in advance for your help.
> 
> DC
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
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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