[BioC] limma 2.2.0 - decideTests heirarch/nestedF + BH correction , small bug

[Ariel Chernomoretz]

Hi,

I think I found a small bug in decideTests
when heirarchical or nestedF methods are selected in conjunction with 
adjust.method="BH" (the new default value).

In both cases there is a problem with the 'switch' command.

 
In adjust heirarchical:
	51                 a <- switch(adjust.method,
	52                         none=1,
	53                         bonferroni=1/n,
	54                         holm=1/(n-i+1),
	55                         BH,fdr=i/n               <-------  BH=i/n,fdr=i/n
	56                 )

In adjust nestedF:
     	65                 a <- switch(adjust.method,
     	66                         none=1,
     	67                         bonferroni=1/n,
     	68                         holm=1/(n-i+1),
     	69                         fdr=i/n               <------- BH=i/n,fdr=i/n
     	70                 )


btw, the p.adjust function of statmod package  makes no distinction between BH 
and fdr methods, why introduce such distinction in limma? (or am I missing 
something?)

regards, and thanks for an excellent tool!

Ariel./


-- 
Ariel Chernomoretz, Ph.D.
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