[BioC] multiple comparison adjustment of p values in LIMMA

[Shi, Tao]

Dear Gordon and list,

Could you please explain why the multiple comparison adjustment procedure implemented in limma (i.e. decideTests) only do adjustment across genes but not across treatment contrasts within a gene?   I found one of your earlier replies related to this here ( https://stat.ethz.ch/pipermail/bioconductor/2012-November/049385.html ):

"Post hoc tests are done in limma using decideTests(), and many options are 
offered.  You won't find classical methods like TukeyHSD though, because 
limma isn't doing classical Anova and because methods like TukeyHSD don't 
generalize well to high-dimensional datasets like microarrays."

Could you please elaborate on this?  Take a 1000-gene data set with 3 treatment groups as an example, if you're doing all 3 pair-wise comparisons, it's 3000 tests.  One would think that controlling FDR for all 3000 tests is quite different from controlling FDR for 1000 tests per comparison.  If I only have a dataset with 50 genes, does this change your statement I cited earlier?


Thank you very much!

Tao