[BioC] Partial F-test using LIMMA

Gordon K Smyth smyth at wehi.EDU.AU
Wed Mar 9 13:33:39 CET 2005

> Date: Tue, 08 Mar 2005 09:15:49 -0700
> From: David Henderson <DNADave at U.Arizona.Edu>
> Subject: [BioC] Partial F-test using LIMMA
> To: bioconductor at stat.math.ethz.ch
> Without hacking into the code behind LIMMA, is there a way to perform
> partial F-tests for groups of variables outside of creating complicated
> contrast matrices?  I have an experiment involving fixed time points
> where the researcher would like to test these two hypotheses: H0_1: Is
> any one of the early time points different from the other early time
> points; and H0_2: Is any one of the late time points different from the
> other late time points.  It should be obvious that this is best attacked
> using a partial F, but how to implement this in LIMMA??

There is no way to compute F tests in limma other than by specifying contrast matrices.

Feel free to explain a syntax which would be simpler.


> Thanks!!
> Dave H
> PS I'm in digest mode and will reply when I receive the digest.
> Alternatively cc me on your reply to the list.
> --
> David A. Henderson, Ph.D.
> Assistant Professor of Animal Genetics, CALS
> Assistant Professor of Biostatistics, AZCOPH
> Member, The Bio5 Institute http://www.bio5.org
> 231 Shantz Building
> Department of Animal Sciences
> The University of Arizona
> Tucson, AZ 85721
> Phone: (520)626-8903
> Fax: (520)621-9435
> DNADave at U.Arizona.Edu
> http://dnadave.cals.arizona.edu/

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