>[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 >Sainte-Foy, Qc >G1V 4G2 >(418)-525-4444 ext 46339