[BioC] nested design in limma?

Gordon K Smyth smyth at wehi.EDU.AU
Tue Feb 21 08:37:22 CET 2006

Hi Jenny,

This design is qualitatively the same as the "duplicate spot" situation, where the treatment is
applied at the array level but the measurements are made on multiple spots per array.  In your
case, treatments are applied to dams but measurements are made on multiple offspring.

Hence you can use the duplicateCorrelation() function in limma with dam as the block.

Best wishes

On Tue, February 21, 2006 6:03 am, Jenny Drnevich wrote:
> 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
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu

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