[BioC] decideTests with nestedF

[Lei Jiang]

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
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