[BioC] nested design in limma?

[Jenny Drnevich]

Hello,

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?

Thanks,
Jenny

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

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1201 W. Gregory Dr.
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e-mail: drnevich at uiuc.edu