[BioC] Limma question: Single channel repeated measures

[Gordon Smyth]

At 06:10 PM 20/08/2004, Nicholas Lewin-Koh wrote:
>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?

Don't the duplicate probes and the repeated scannings of the same array 
also introduce error strata? Anyway, this is too complicated for limma.

Gordon

>Thanks
>Nicholas