I am trying to understand the details of the RMA algorithm in terms of log
transform. The probe level data obtained from ReadAffy is obviously not log
transformed, so in the 3 steps:

1. background subtraction:
2. quantile normalization:
3. median polish summarization.

should the algorithm work on raw data (without log transform) or log
transformed data for these steps? I was trying to judge from the output
data, but realize that it is not obvious to figure out because the
following two options both give log transformed output:
(take quantile normalization as example)

A. quantile normalization on raw data and then log transform
B. quantile normalization on log transformed data

Thanks,

-Jack

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