[BioC] justRMA and logarithm transformation

Ben Bolstad bmb at bmbolstad.com
Fri Mar 16 14:59:19 CET 2007

The log2 transformation happens after background and normalization
during the summarization stage. Turning normalization=FALSE or
background=FALSE or both FALSE will have no effect on whether it gets
log2 transformed.



On Fri, 2007-03-16 at 11:53 +0000, 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.
> Thanks very much,
> Alex Richards
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