In limma manual, the example of time course experiment (Section 9.6) the target frame showed 2 replicates of 0hr wt and mutant but why it was not considered in the levels or in design? Can anyone please explain the discrepancy? The example, "we consider here a two-way experiment in which time course profiles are to be compared for two genotypes. Consider the targets frame
FileName Target File1 wt.0hr File2 wt.0hr File3 wt.6hr File4 wt.24hr File5 mu.0hr File6 mu.0hr File7 mu.6hr File8 mu.24hr
The targets are RNA samples collected from wild-type and mutant animals at 0, 6 and 24 hour time points. This can be viewed as a factorial experiment but a simpler approach is to use the group-mean parametrization.
> lev <- c("wt.0hr","wt.6hr","wt.24hr","mu.0hr","mu.6hr","mu.24hr") > f <- factor(targets$Target, levels=lev) > design <- model.matrix(~0+f) > colnames(design) <- lev > fit <- lmFit(eset, design)