[BioC] log transform in RMA normalization

Benjamin Bolstad bmb at bmbolstad.com
Thu Jan 24 15:47:03 CET 2013


the log transformation occurs at the summarization step. i.e. both background correction and quantile normalization occur on the natural scale.

Ben


On Jan 24, 2013, at 6:43 AM, Jack Luo <jluo.rhelp at gmail.com> 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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> 
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