[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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