[BioC] log transform in RMA normalization

[Benjamin Bolstad]

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
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor