[BioC] GCRMA with custom chips

[James W. MacDonald]

Daniel Pick wrote:
> Hello,
> I am running RHEL 3, R 2.2, BioC 1.7, gcrma2.2
> I would like to apply gcrma to a custom chip, but I don't know how to tell
> gcrma to look on my local box for the probe sequence information.  If
> anyone knows how to do this, I would appreciate any assistance you can
> give.

First you have to make a probe package (have you done this?). If not, 
you have to use makeProbePackage() in the matchprobes package. Leave 
pkgname set to NULL so the package will get the correct name. After 
making the package, install using R CMD INSTALL, and you should be good 
to go.

HTH,

Jim


> 
> Dan
> 
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-- 
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