[BioC] Methods in decideTests (limma)

[Michal Kolář]

Dear list,

I would like to ask on the theory behind various methods in  
decideTests. The method "separate" is clear to me, giving p-value  
adjustment for each contrast separately. The method "global" may be  
used presumably when there are two or more contrasts of similar  
strength in the experiment. The method "nestedF" seems to me similar  
to the "global", yet it considers for p-value adjustment only those  
genes for which F-test is significant after p-value correction  
(roughly said). Is that correct? And finally, the method  
"hierarchical" considers for the final p-value adjustment only those  
genes/contrasts for which adjusted p-value (of the gene in the  
contrast treated separately) is smaller than some cut-off. Is that  
right?

My next question is whether any of the methods "global",  
"hierarchical" or "nestedF" can be used to correct p-values for  
contrasts that have different strength (different number of expected  
DEGs)? In my case 'different' means hundreds of DEGs for one contrast  
and tens for the other.

Can I find more details on the methods in some reference?

Cheers,
Michal

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Michal Kolář
Academy of Sciences of the Czech Republic
Institute of Molecular Genetics