[BioC] limma: decideTests, which option to chose?

[kerick@molgen.mpg.de]

Dear all, 
 
to the best of my knowledge these questions haven't been posed so far; I 
apologize if I didn't dig deep enough.  
I am seeking advice on which option to choose from the decideTests function in 
limma. Since the methods nestedF, heirarchical, global and separate (all using 
fdr adjustment) give pretty different numbers of genes being classified as 
significant I wonder which choice is statistically speaking the most stringend 
and which is the least stringend. Any idea how to line up all choices with 
regard to increasing stringency? nestedF < heirachical < global < 
separate  ..maybe? 
practical questions: 
We performed an experiment which tries to answer seven questions(~ 7 
contrasts). 
I chose the nestedF option to get a fair amount of "differentially regulated" 
genes for each contrast to then perform fisher.test analysis on geneontology 
groups for each contrast separately. 
Then I chose the heirarchical option to have a closer look at the genes one by 
one for each contrast at hand.  
Any doubts concerning this strategy? 
 
I appreciate any comment, 
Best regards, 
 
Martin