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! [[alternative HTML version deleted]]