[BioC] median polish vs mas

[James MacDonald]

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()
function.

Best,

Jim


James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> 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
the 
extra between array step imposed by median polish give the possibility
of 
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
(Statistics)
University Park, PA 16802-2111

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