[BioC] Filter before? Filter after? With maanova

[Robert Gentleman]

Hi Loren,
  The only results that I am aware of suggest that using non-specific
filtering (as described in the Case Studies book, and a hopefully soon
to appear paper) is in general of benefit.
   Filtering after you fit a model is not appropriate - at that point
you must rely on what ever form of p-value adjustment you prefer.

   best wishes
     Robert


On Sat, Jul 4, 2009 at 5:07 PM, Loren Engrav<engrav at u.washington.edu> wrote:
> I have 10,000 probe sets that I am processing with mixed linear regression
> and the maanova package
> I can filter in various ways, ie does human expression match porcine
> expression?, and reduce the number of probe sets
> Is it more valid to filter before doing the regression, or after?
> Thank you
> --
> Loren Engrav, MD
> Univ Washington
> Seattle
>
>
>
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org