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

[Gordon Smyth]

>[BioC] limma 2.2.0 - decideTests heirarch/nestedF + BH correction , small bug
>Ariel Chernomoretz ariel.chernomoretz at crchul.ulaval.ca
>Wed Nov 23 16:55:20 CET 2005
>
>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                 )

This is not a bug. It is a legal R short-hand for what you have written.

>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                 )

On the other hand, this is a bug. It has been fixed already in limma 2.3.6, 
but thanks for reporting it anyway. Unfortunately the bug is still in 
Bioconductor release 1.7, but the easy work-around is just to use "fdr" 
instead of "BH".

>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?)

limma does the same as p.adjust. It treats "fdr" and "BH" as the same, but 
has to accept either as input.

Best wishes
Gordon

>regards, and thanks for an excellent tool!
>
>Ariel./
>
>
>--
>Ariel Chernomoretz, Ph.D.
>Centre de recherche du CHUL
>2705 Blv Laurier, bloc T-367
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