Entering edit mode
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