[BioC] Limma question: Single channel repeated measures

[Nicholas Lewin-Koh]

Hi,
first the design:
I have 12 hand spotted arrays in 3 blocks with 4 treatments in each
block.
Each array is scanned at 2days, 3days and 4days exposure (this is
phospholuminescince).
Each probe is replicated twice on the array in neighboring spots, so the
array
rows look like

 ** ** ** ...... **
 ** ** ** ......
 :
 :
 :

If this were a univariate response eg, one gene, I would probably just
use a split plot, something like

Block
treatment (Block)
Block * Treatment (Error1)
Time
Time*Treatment
Time*Block + Time*Block*Treatment (Error 2)

and just concentrate on the treatment effect before
modelling the covariance and mixed effects, and hope it
is a reasonable approximation. 

Is it possible to do something like this in limma? How do I force 
it to get the correct error, or is this a bad idea?


Thanks
Nicholas