[BioC] ttest or fold change
Rafael A. Irizarry
ririzarr at jhsph.edu
Sat Dec 13 17:59:12 MET 2003
in my experience with affymetrix microarryas the t-test is close to
power-less with only 3 replicates. fold-change works much better. things
like sam (see siggenes package for sam-stat and limma package for sam-like
stats) are much better as well. if you do use a t-test make sure to
look at a volcano plot (-log p-value versus average log fold change).
typically you see many many genes with very small pvalues but log
fold-chages very close to 0. these are likely not of interest (the
denominator of t-test was small by chance).
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?
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