[BioC] justRMA and logarithm transformation

[Alexander Richards]

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