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Dear Jim,<br><br>
The reason I ask is that I <b><i>have</b> </i> been using expresso with
"mas". But I recently had a paper returned with the
comment that median polish was "known to be better". If
so, I should probably use it. The reviewer appears to have based
his/her remarks on the fact (mentioned in the review) that median polish
is the "default".<br><br>
If the decision to use median polish in justRMA was arbitrary, I would
like to know this, since I am currently in the process of redoing all of
the statistical analyses and tables in the paper (which is pretty
time-consuming). The main reason we are redoing everything, rather
than defending our decision to use "mas" is that I certainly
have no evidence that Tukey's biweight is "better" except for
the heuristic about over-normalization, and I figured in the long run we
will have fewer arguments with reviewers if we use the default.
<br><br>
I should not have said that median polish is the "default" in
justRMA, since it is the only method available, but I do think that its
use in justRMA is an endorsement meaning that anyone doing anything
besides Affy-type MAS5 or justRMA or justGCRMA (if this is available) is
going to be asked to justify what they are doing with more
stringency.<br><br>
--Naomi<br><br>
<br><br>
At 10:49 AM 5/17/2004, James MacDonald wrote:<br>
<blockquote type=cite class=cite cite>The default (and only) option for
justRMA is medianpolish because<br>
justRMA is designed to *just* do *RMA*, which is a quantile<br>
normalization followed by medianpolish. The only reason justRMA
exists<br>
is to allow people with less RAM to be able to do rma.<br><br>
If you think a quantile normalization followed by Tukey's biweight
will<br>
do better than rma, you can certainly do that using the expresso()<br>
function.<br><br>
Best,<br><br>
Jim<br><br>
<br>
James W. MacDonald<br>
Affymetrix and cDNA Microarray Core<br>
University of Michigan Cancer Center<br>
1500 E. Medical Center Drive<br>
7410 CCGC<br>
Ann Arbor MI 48109<br>
734-647-5623<br><br>
>>> Naomi Altman <naomi@stat.psu.edu> 05/17/04 10:15AM
>>><br>
I have been wondering why the default in justRMA is <br>
summary.method="medianpolish" instead of "mas"
which is Tukey's <br>
biweight. Since we are already doing quantile normalization,
doesn't<br>
the <br>
extra between array step imposed by median polish give the
possibility<br>
of <br>
masking differential expression?<br><br>
Naomi S.
Altman
814-865-3791 (voice)<br>
Associate Professor<br>
Bioinformatics Consulting Center<br>
Dept. of
Statistics
814-863-7114 (fax)<br>
Penn State
University
814-865-1348<br>
(Statistics)<br>
University Park, PA 16802-2111<br><br>
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<x-sigsep><p></x-sigsep>
Naomi S.
Altman
814-865-3791 (voice) <br>
Associate Professor <br>
Bioinformatics Consulting Center<br>
Dept. of
Statistics
814-863-7114 (fax) <br>
Penn State
University
814-865-1348 (Statistics) <br>
University Park, PA 16802-2111<br>
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