I was afraid you would say that, ie must filter before fitting I have been filtering on human expression "by hand" and more probe sets to examine is lots of work; so letting Fs cut first saves time; but if not appropriate then not appropriate So yesterday I set up a Filemaker script that passed testing and so hit the "do" button; is now 50% done after 1.5 hours but this will be better than the manual method So will filter before fitting Thank you > From: Robert Gentleman <rgentlem at="" fhcrc.org=""> > Date: Mon, 6 Jul 2009 09:43:32 -0700 > To: Loren Engrav <engrav at="" u.washington.edu=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] Filter before? Filter after? With maanova > > 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 >> >> >> >> ? ? ? ?[[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > > > -- > 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