[BioC] ttest or fold change

Michael Newton newton at biostat.wisc.edu
Sat Dec 13 17:27:52 MET 2003


My own calculations have also shown a lack of sensitivity of both
t-testing and other approaches when we have few replicates.  You
might be interested in a mixture approach that seems promising.
See http://www.stat.wisc.edu/~newton/papers/abstracts/tr1074a.html
for code and a paper.

Michael Newton

p.s. That site contains a major revision of the report I released
  last January, with code etc recently updated; aiming for
  Bioconductor soon!

On Sat, 13 Dec 2003, Jason Hipp wrote:

> I am comparinga relatively homogeneous cell culture to another that has been treated, and am using RMA.
> I only have 3 replicates of each.  Would you recommend a 2 tailed equal variance t test?
> I also thought I read that with such few replicates, a fold change would be better than a t test?
> If I get a t test of .0001, and a fold change of 1.2, is this a reliable change using RMA?
> Thanks,
> Jason
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