Hi,
we have recently finished a large microarray experiment on HGU133plus2 (each experimental point is in triplicate) made of 4 different compound treatments on the same cell line investigated at 0, 1,2,3,4,5,6,24 hours.
We have done a full randomization of experimental steps. We were quite disappointed when we observed that, after&nbsp;RMA calculation (quantile normalization),&nbsp;in PCA&nbsp; data are grouped also on the basis of the day of cRNA synthesis.
We would like to investigate this experiment using the timecourse package. Does anybody know if the model implemented in the timecouse package will handle this “day effect”?
&nbsp;
Is it a reasonable option to normalize first the data grouped by the "day of cRNA synthesis" and then, after combining all in a unique exprSet, performing a further normalization?
&nbsp;
Best
Raffaele
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