[R-sig-ME] Problems with formula for highly pseudoreplicatemixed-effects system

[David Duffy]

On Thu, 17 Sep 2009, Matthias Gralle wrote:

>
> I have been trying for some weeks to state the correct design of my 
> experiment as a GLM formula, and have not been able to find something 
> appropriate in Pinheiro & Bates 2000 or with any of the local R users, so I 
> am posting it here and hope somebody can help me.
>
> In each experimental condition, described by
> 1) gene (10 levels, fixed, because of high interest to me)
> 2) species (2 levels, fixed, because of high interest)
> 3) day (2 levels, random)
> 4) replicate (2 levels per day, random),
>
> I have several thousand data points consisting of two variables:
>
> 5) FITC (level of transfection of a cell)
> 6) APC (antibody binding to the cell)
>
> ...pseudoreplication, and with 
> 200000 data points in the original data set, any interaction will be 
>
What do you mean by pseudoreplication -- repeated measures?  Don't you 
want something like APC ~ gene + FITC + (FITC|gene) + species + (1|day) + 
(1|replicate), where your interest is in the random regression FITC|gene?. 
Alternatively/equivalently, how about testing for homogeneity of the 
FITC-APC (partial) correlation coefficients across 10 gene strata (what do 
these look like?).  The latter is natural for a multigroup SEM.


I hope I understand what you are talking about

Cheers, David Duffy.