[BioC] median polish vs mas

James MacDonald jmacdon at med.umich.edu
Mon May 17 16:49:18 CEST 2004

The default (and only) option for justRMA is medianpolish because
justRMA is designed to *just* do *RMA*, which is a quantile
normalization followed by medianpolish. The only reason justRMA exists
is to allow people with less RAM to be able to do rma.

If you think a quantile normalization followed by Tukey's biweight will
do better than rma, you can certainly do that using the expresso()



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Naomi Altman <naomi at stat.psu.edu> 05/17/04 10:15AM >>>
I have been wondering why the default in justRMA is 
summary.method="medianpolish"  instead of "mas" which is Tukey's 
biweight.  Since we are already doing quantile normalization, doesn't
extra between array step imposed by median polish give the possibility
masking differential expression?

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

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