Hi

Googling the list shows this up to be a rather hot topic, but I just
wanted to ask a few more questions.

Firstly, it seems the plan for tackling time course data within limma is
to treat each time-point/treatment combination as a coefficient to be
estimated.  Thus, to ask "which genes are changing over time", one must
fit contrasts that compare every single time point to every other time
point, pairwise, and look for any gene that is significant in one or
more of those comparisons.  Is that correct?

I am also a tad confused by the documentation, which states (on page
47):

"> cont.wt <- makeContrasts(
+ "wt.6hr-wt.0hr",
+ "wt.24hr-wt.6hr",
+ levels=design)
> fit2 <- contrasts.fit(fit, cont.wt)
> fit2 <- eBayes(fit2)

Any two contrasts between the three times would give the same result.
The same gene list
would be obtained had "wt.24hr-wt.0hr" been used in place of
"wt.24hr-wt.6hr" for example."

I'm confused why "wt.24hr-wt.0hr" and "wt.24hr-wt.6hr" would give the
same gene list.  The first looks for differences in wt between time
points 0 and 24, and the second looks for differences between time
points 6 and 24.

I guess, to me, this all seems a bit verbose and difficult, particularly
for large time-course experiments where many biologists want to subset
their data to those genes that change over time and thus want to ask the
question "does time have an effect on the expression of my gene?" and
are not particularly bothered, at this stage, which particular time
points those genes differ at.

Thanks in advance
 
Mick





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