[BioC] Question about F test in limma

[Lisa Mijung Chung]

Dear limma expert,
I have a question about performing F-test (with several groups) on limma.
If I have 3 targets (using Affy chips) called RNA1, RNA2, RNA3 and
want to get F statistic to test
H0: no difference vs. H1: at least one target is different,
(Similar with example on Section 8.6 of limma user guide at pp.42-43)

Should I construct my contrast matrix:
> makeContrasts(RNA2-RNA1, RNA3-RNA2, RNA3-RNA1) # with all pairwise comparisons

or would it be fine only with:
> makeContrasts(RNA2-RNA1, RNA3-RNA2)            # comparisons of two adjacent pairs

With best wishes,
Thank you.


-- 
Lisa Mijung Chung
Graduate Student, Biostat Trainee
Department of Statistics, UW-Madison
Web: www.stat.wisc.edu/~lchung