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]]

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