[R-sig-ME] mixed-effects model specification question

[Andrew Robinson]

Mark,

You should talk to a local statistician about this, but I think that
you can probably average across the measurements within each rat, if
all you are interested in is a treatment effect.  For the analysis of
treatment the relevant unit of replication should be the rat, in any
case.

(Does anyone have any thoughts on why that might be a bad idea?)

Also if I understand your design, there are three batches per rat.  I
suspect that using Rat/Tissue would lead to an over-parametrized
model, if my interpretation is correct.  My guess is that Rat should
be adequate.

Final points

1) My speculations would be better-informed if you showed us the
   output of the model that you proposed - fyi :) .

2) You could try all three configurations and see if it makes any
   difference to the inference of interest.  I suspect that it will
   not.

I hope that this helps,

Andrew

On Tue, May 06, 2008 at 10:23:08AM -0400, Mark Kimpel wrote:
> 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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-- 
Andrew Robinson  
Department of Mathematics and Statistics            Tel: +61-3-8344-6410
University of Melbourne, VIC 3010 Australia         Fax: +61-3-8344-4599
http://www.ms.unimelb.edu.au/~andrewpr
http://blogs.mbs.edu/fishing-in-the-bay/