[BioC] justRMA and logarithm transformation

[James W. MacDonald]

Hi Alexander,

Alexander Richards wrote:
> Hi,
> 
> I'm a PhD student at Cardiff University, working on neuropsychiatric conditions by using clustering
> techniques on microarray data. I've dug through the archives, but haven't been able to find a
> definite answer to my question.
> 
> When using justRMA to process microarray data from CEL files, when is the log2 transformation
> applied? Does it occur as part of the normalisation or background correction steps, and so will not
> occur if 'normalization=FALSE' or 'background=FALSE' is used? Or is it an inherent part of the
> process? I believe it's the latter, but I don't know for sure.

You _could_ just run justRMA() on some celfiles with normalize = FALSE 
and background = FALSE to see for yourself.

But since you asked, it is an inherent part of the process. You wouldn't 
want to do medianpolish on unlogged data.

Best,

Jim


> 
> Thanks very much,
> 
> Alex Richards
> 
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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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