[BioC] nested design in limma?
drnevich at uiuc.edu
Mon Feb 20 20:03:20 CET 2006
I was wondering if there was any (easy) way to handle a nested design in
limma. I looked in the Bioconductor archives, but the only references to
nested designs weren't really nested - one was just a factorial design, and
the other was a repeated measurement design, which could be done in limma
as a blocking variable. In this experiment design, the treatments (infected
and control) were made on the dams, but the effects were measured on
multiple offspring per dam; hence dam is nested within treatment. In SAS
terminology (forgive me...), the model would look like this:
log2_expression = treatment + dam(treatment) , with dam as a random
variable. The test statistic for treatment should now be formed using the
variance due to dam(treatment) and not the error variance. Can limma be
made to handle this sort of design?
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 uiuc.edu
More information about the Bioconductor