[BioC] bg.adjust.gcrma

[James W. MacDonald]

zhxiaoyu at ucla.edu wrote:
> Hi all,
> 
> We are using an Affy tiling array and would like to try gcrma for background
> correction only. I got a CDF file from Affy and made a CDF env (not a package)
> which worked fine for bg.correct.rma, but not bg.adjust.gcrma in BioC 1.7 -
> instead of using the environment I made it kept trying to find one in the BioC
> repository. I also tried modifying gcrma as Zhijin suggested before but run
> into the same problem. Is there any way to make bg.adjust.gcrma use my local
> env or do I have to make a package? Any input would be much apppreciated.

You don't need to make a package, although that would be easiest in the 
long run.

The problem here is that the function getCdfInfo() is a bit inconsistent 
as to what it expects the cdfenv to be called. In your case, when you 
want to find an environment in the .GlobalEnv, you will be calling 
getCdfFromEnvironment(), which looks for cdfName(abatch), where abatch 
is your AffyBatch. Therefore, you have to name your cdfenv correctly or 
it will not be found.

The best way to determine what you should call your env is to call 
cdfName on an AffyBatch containing tiling array raw data.


HTH,

Jim




> 
> Best,
> 
> Xiaoyu
> 
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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