Question: decideTests with nestedF

0

Lei Jiang •

**20**wrote:
Dear all,
I am comparing two time points (6 time points) data under different
conditions.
I want to look for genes that show different pattern under different
conditions.
I constructed contrasts as in the user's guide (diff=cond1-cond2 at
all pairs
of time points) and generated MArrayLM object okay.
My questions come with decideTests with "nestedF".
1. how is the classification done exactly?? I found a much smaller set
of genes
using decideTests(nestedF, p=0.01) versus p.adjust(fit$F.p.value)<0.01
2. The TestResults matrix doesnt really make sense. for example,
places where
the matrix shows 1 as upregulation, dont necessarily have positive M
value or
doesnt show a p.value < 0.01?? What do I miss here?? really
confused...
3. p.value and adjust.method parameter in the decideTests are applied
to F stat
or to the individual p value at each gene at each contrasts.
I hope I made the questions clear. Need help desperately, since
there's not
much document on this. Other suggestions for this type of analysis are
also
welcome.
Thank you.
Lei Jiang
Department of Chemsitry
University of Washington
Box 351700
Seattle, WA 98195
Phone: 206-616-6882
Fax: 206-685-8665