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Malard, Joel M
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@malard-joel-m-917
Last seen 10.2 years ago
This is a naďve question. Is there some BioConductor package to
estimate mixed models on Affymetrix data?
I have a 2 x 2 design, treatment versus control at two labs. There are
strong (lab) batch effect that can be seen by clustering the data. So
far I have computed RMA (and GCRMA) values for each lab separately,
normalized across arrays using limma's normalizeBetweenArrays
(quantile) and generated lists of potentially differentially expressed
genes via lmFit, eBayes and TopTable. I would like to estimate how
much of a batch effect remains.
>From my numeralogist roots, I know that a mixed model across all
arrays need not give the same estimates as a linear model of the
residuals from linear models derived for each lab. Any pointer on how
other people handle batch effects would be most useful and most
welcome.
With best regards to all,
Joel M. Malard, Ph.D.
Scientist IV
Pacific Northwest National Laboratory
Tel: +509 372-6539 Fax: +509 375-2604
Battelle Boulevard, PO Box 999
Mail Stop K6-08
Richland, WA 99352
"I love the audacity of those who have everything to lose from it; the
moderation of those who have nothing to gain from it." Rostand, Jean
(1894-1977)
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