[BioC] Two-color factorial design, common reference

[Sean Davis]

Sorry for another anova-like question, but I have a set of two-color
experiments with two variables (time (4 and 8 hours) and treatment(two
levels)), but they are hybed to a common reference (untreated line).  Does
this design look correct (for use in limma)?

Ref 4hr  8hr    TrtA  Trtb   Treated
-1   1    0     1      0    1
-1   1    0     1      0    1
-1   1    0     0      1    1
-1   1    0     0      1    1
-1   0    1     1      0    1
-1   0    1     1      0    1
-1   0    1     0      1    1
-1   0    1     0      1    1

I am interested in knowing genes differentially expressed in the treated
cells, treatment A vs. treatment B, 4hr vs. 8hr.  I would do contrasts
something like:

MakeContrasts(Treated,4hr-8hr,Trta-Trtb,levels=design)

When I do the 4hr-8hr contrast, for example, does this "control" for the two
different treatments?  In other words, if there are different magnitude of
effects due to the treatments, but the genes changing are the same at 4 and
8 hrs, will the 4hr-8hr still be significant?

Thanks,
Sean