[BioC] Limma question: Single channel repeated measures

[Nicholas Lewin-Koh]

Hi,
Thanks for the quick reply, yes the replicate spots would add extra
error strata, I was trying to simplfy, and should have clarified. I was
referring to time as the repeated scannings. 

Any suggestions about what I might use, before I dive into lme4 and
write something
home grown?

Thanks for any suggestions, the question of interest is just paired
comparisons 
between treatments, so I would be happy just doing moderated t
statistics if the 
efficiency is ok and the bias not too great.

Nicholas

On Fri, 20 Aug 2004 18:57:57 +1000, "Gordon Smyth" <smyth at wehi.edu.au>
said:
> 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
>