[BioC] how to test for genes of interest?
drnevich at illinois.edu
Thu Jul 24 17:14:33 CEST 2008
I've always heard that one of the ways "around" the multiple testing
problem of microarrays is for you to a priori identify a particular
list of genes you're interested in, and then you only have to do the
multiple test correction for this smaller list. I've never done this
in practice, and I'm not sure at what point in the analysis it's
proper to pull out just the smaller list. Obviously, all the data
preprocessing and normalization will be done with all the genes, but
should I pull out the genes before fitting the model, or after
fitting the model right before the multiple test adjustment? I'm
using the eBayes() shrinkage in limma, so which genes are in the
model will make a big difference in the outcome.
I'm thinking it would be best to keep all the genes in the model, and
then split them out into two groups (genes of interest and all the
rest) and do a FDR correction separately for each group. What do you think?
Jenny Drnevich, Ph.D.
Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign
1201 W. Gregory Dr.
Urbana, IL 61801
e-mail: drnevich at illinois.edu
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