[BioC] unbalanced factorial design

Kenny Ye kye at ams.sunysb.edu
Thu Feb 5 01:02:19 MET 2004

I am not sure about if bioconductor includes any functions for
mixed-effect models. there are several packages in R handles mixed-effect 
models, the most complete one is nlme. But SAS Proc MIXED probably is the
better way to go. 

in my opinion, slightly non-balancing does not affect your inference very
much. A good reference is Milliken and Johnson, Analysis of Messy Data,
Volumn I;


Kenny Ye
Assistant Professor
Department of Applied Math and Statistics
SUNY at  Stony Brook
Stony Brook, New York 11794-3600
Phone (631)632-9344
Fax   (631)632-8490

On Wed, 4 Feb 2004, Christian Landry wrote:

> Hi,
> I am analyzing microarray data from a factorial design, with treatments and 
> genotypes. I would like to know if some of you have experience with 
> Bioconductors packages doing Mixed-Model Anova that deal with unbalanced 
> design, i.e. not the same number of replicates for each treatment-genotype 
> combination. I am particularly interested in the interaction between 
> treatment and genotype so I know that the design is an issue. Any references?
> Thanks in advance,
> Christian
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