[BioC] Odd contrast; does it make statistical sense?

[Ryan]

On Thu Jan 23 21:10:27 2014, Aaron Mackey wrote:
> But had he more simply coded the samples as belonging to two groups,
> AB and CD, then the dispersions could be larger, and the AB vs. CD
> mean differences could be less significant than in his four-subgroup
> design.  I think that was the intent of Ryan's question.  Is it fair
> to stratify along a priori expected subgroupings to minimize variance
> and then ask group-level questions?  As you later say, if there is
> "lots of DE" between A vs. B and/or C vs. D (read: larger group-wise
> variance) then the test may need to be "carefully interpreted".

Yes, this is exactly what I am asking.

-Ryan