[BioC] Limma and randomized block design for time-course microarray experiment

[Serge Eifes]

Dear all,

We have performed a time-series experiment (2h, 6h, 10h, 48h,  
) on
dual-channel arrays where we want to compare gene expression between treated
and time-matched untreated cells. For every time-point three hybridizations
were performed including one dye-swap. Each time-course was hybridized at
the same time. 

So for a given time point we have 3 different microarrays comparing:
Tx -> Ux
Tx ->Ux
Ux ->Tx

T=treated cells ; U=untreated cells at corresponding time-point ; x=given
time-point.

Is it possible in this case (unbalanced design) to use randomized blocks in
LIMMA to estimate variability between the three microarray batches
(time-courses)? 

If affirmative, the R code I would use looks as follows:

> design = cbind( T2vsU2=c(1,1,-1,0,0,0,0,0,0,0,0,0),
> T6vsU6=c(0,0,0,1,1,-1,0,0,0,0,0,0),
> T10vsU10=c(0,0,0,0,0,0,1,1,-1,0,0,0),
> T48vsU48=c(0,0,0,0,0,0,0,0,-0,1,1,-1))
> blocks = c( 1,2,3,1,2,3,1,2,3,1,2,3)
> dupcor = duplicateCorrelation(MA, design=design, block=blocks)

Is this piece of code appropriate to model the randomized blocks (the three
time-courses)?


Many thanks in advance,

Serge


Serge Eifes
Laboratoire de Biologie Moleculaire et Cellulaire du Cancer (LBMCC)
Hopital Kirchberg 
9,rue Edward steichen 
L-2540 LUXEMBOURG