[BioC] decideTests with nestedF
lj22 at u.washington.edu
Wed Jul 27 01:02:05 CEST 2005
I am comparing two time points (6 time points) data under different
conditions. I want to look for genes that show different pattern under
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
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
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
Department of Chemsitry
University of Washington
Seattle, WA 98195
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