Dear all,

I am interested in performing a time course experiment for a two color
microarray. As the example shown in the userguide is just for one color
arrays, I was wondering if the following code is correct for the same
example but assuming that we have a two color array (example extracted from
8.8 Time Course Experiments, limma userguide).

Assuming a common reference to simplify the set:

 FileName Cy3 Cy5  File1 wt.0hr Ref  File2 wt.0hr Ref  File3 wt.6hr Ref
File4 wt.24hr Ref  File5 mu.0hr Ref  File6 mu.0hr Ref  File7 mu.6hr Ref
File8 mu.24hr Ref


> lev <- c("wt.0hr","wt.6hr","wt.24hr","mu.0hr","mu.6hr","mu.24hr")
> f <- factor(targets$Cy3, levels=lev)
> design <- model.matrix(~0+f, ref= "Ref")
> colnames(design) <- lev
> fit <- lmFit(eset, design)

Thank you!

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