[BioC] RMA

Naomi Altman naomi at stat.psu.edu
Mon Jan 30 22:42:28 CET 2006

Could someone please clarify some points about RMA normalization by 
confirming or correcting my summary below:

1) The background correction uses only the PM probes.  Essentially, 
it looks for the probes below peak of the PM probe distribution, and 
uses these to estimate the parameters of the mixture model.
2) The quantile normalization is done on the background corrected PM probes.

Thanks.  I did not find the details spelled out in the papers.

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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