Question: log transform in RMA normalization

0

Jack Luo •

**400**wrote: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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modified 6.2 years ago
by
Ben Bolstad •

**1.2k**• written 6.2 years ago by Jack Luo •**400**