[BioC] Harsh results using limma!

[A.J. Rossini]

"michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk> writes:

> I am extending the argument to the larger case where I might have plenty
> of replicated experiments and still want to find significant genes
> amongst sub-populations.  I've had one e-mail which shows that this is
> possible, so I am happy.
>
> What everyone needs to understand, though, is that on one hand we have
> statisticians saying we should have 100s of replicates and on the other
> hand a legal obligation and an ethics committee saying we have to use as
> few animals as possible.  There's also an element of "don't shoot the
> messenger"; I didn't design the experiment, in fact the 1st I heard of
> it was when I was asked to analyse it (hands up on the list who's
> experienced that....).  I *know* there should be more replicates, but at
> the end of the day, I need to make as much use of the data I have as is
> possible, and any number of "Argh"'s and "you need more replicates"'s
> are not going to help me :-D

We run into the same problem with clinical trials, which is in a sense
the framework that you are using (biological replicates).

When you throw in the "cost, ethics, legal obligations, IRBs..."
issues, having statistical power is more critical.  And if you can't
find results, one might argue that the experiment shouldn't be done
(taking the harsh other view that a experiment with a highly probable
inconclusive result, when ethics raise their ugly head, is not worth
doing).

Statistical designs are always are a tradeoff.

best,
-tony

-- 
Anthony Rossini			    Research Associate Professor
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC  (M/W): 206-667-7025 FAX=206-667-4812 | use Email

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