[BioC] gcrma and custom chips

[James W. MacDonald]

Daniel Pick wrote:
> Hello,
>     I would like to apply gcrma to a custom chip for which I have the probe
> sequence information.  gcrma appears to automatically go to the Internet to
> search for the appropriate probe package.  How do I override this behavior
> to look for a ProbePackage built and installed locally?

Did you give the probe package a name, or did you accept the default 
one? If you didn't give the probe package the expected name, gcrma() is 
not going to be able to find it. If you passed a name to 
makeProbePackage(), your best bet is to uninstall the existing package, 
and re-make the probe package without passing a name. This will give it 
the default name, which gcrma() will then be able to find.

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
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