Dear Ariel, James MacDonald has pointed out to me that I still didn't get this quite right. Hopefully the treatment of adjust="BH" is finally correct now in limma 2.4.4. >To: "Ariel Chernomoretz" <ariel.chernomoretz at="" crchul.ulaval.ca=""> >From: Gordon Smyth <smyth at="" wehi.edu.au=""> >Subject: [BioC] limma 2.2.0 - decideTests heirarch/nestedF + BH correction >, small bug >Cc: Bioconductor >Date: Thu, 24 Nov 2005 14:51:34 +1100 > >>[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. You're right. >> 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. Oops. For this to be legal R code, I needed "BH=, fdr=1/n". In other words, I forgot one of the "=" signs. >>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". My so-called fix in limma 2.3.6, actually repeated the same bug as for adjust="heirarchical". Both of these should now be correct in limma 2.4.4. Sorry for the confusion. Thanks again for reporting the bug. Cheers Gordon >>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