Perhaps a bit of a newbie question, but I need to get this right. I need to
make sure I am specifying a model correctly. Here is our less-than-perfect
experimental design:

36 rats divided into two treatment groups, i.e. 18 per group

each rat has measurements taken on 3 brain regions, but each brain region
was analyzed in a separate batch (there are strong batch effects) so we
really can't compare the regions per se, but do recognize that the 3 regions
from a single rat have variance above and beyond that accounted for by
technical factors. Since, because of the batch effect we are not going to
look at the effect of brain region, I "think" this should be a considered a
random effect.

So I have rat, treatment, and region(batch) as variables. The only thing I
am interested in getting a p-value for is treatment.

Is the model below correct and can I squeek by with using nlme to get a
p-value (notwithstanding recent threads on this list)?

 myModel <- lme(fixed = geneExpression ~  Treatment,  random = ~1 |
Rat/Tissue)

Thanks,
Mark
-- 
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN 46074

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