[BioC] limma example Weaver Data

[Wenbin Liu]

Dear Gordon and limma users,

I'm struggling to understand the design matrices in
the Weaver Data in the Case Studies section of the
limma User's Guide. 

In the single loop design, there are 4 arrays and 4
conditions (from two time points and two genotypes).
I tried using modelMatrix() with the target from the
example and assigning ref='P11WT'. I would like to
check the effect 'TimeWt' which is the late vs. early
for WT. Unfortunately, I have been unable to get
Gordon's result (topTable result).

Can someone show me how to get Gordon's design
matrices (two of them in that example) by using the
function modelMatrix() and probably plus
makeContrasts()?

Thanks in advance!

Sincerely,
Wenbin