
> Hi,
> we are investingating on Affymetrix Chips the effect of a compound over a time course (1, 2, 3, 4, 5 hours), we also have the mock cells at 1, 2, ,3, 4, 5 hours. All points are biological duplicates.
> Since the experiment was part of a larger one, samples preparation and labelling were randomized .
> Analysing the previously indicated transcription profiles we obeserved that, in PCA, they are clustering by preparation day, hiding the effect of the compound over the time course. 
> There is any way to make limma able to keep in account the "day effect" in the definition of differential expression?
> 
> Thanks,
> 
> Roberta

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