I apologize for the foolish mistake. Of course, the usual t-statistic (assuming equal variances) is equal to Welch's t-statistic (assuming differing variances) if n_1 = n_2, i.e. when both groups have the same size. Ann ---------- Forwarded message ---------- Date: Tue, 17 Jan 2006 18:15:14 +0100 (MET) From: Holger Schwender <holger.schw@gmx.de> To: Ann Hess <hess at="" stat.colostate.edu=""> Subject: Re: [BioC] mt.teststat (multtest) BUG? Hi Ann, that's not a bug. The usual t-statistic (assuming equal variances) is equal to Welch's t-statistic (assuming differing variances) if n_1 = n_2, i.e. when both groups have the same size. Best, Holger > --- Urspr?ngliche Nachricht --- > Von: Ann Hess <hess at="" stat.colostate.edu=""> > An: BioConductor Mail List <bioconductor at="" stat.math.ethz.ch=""> > Betreff: [BioC] mt.teststat (multtest) BUG? > Datum: Tue, 17 Jan 2006 09:20:24 -0700 (MST) > > I am using the function mt.teststat (from multtest package) in R2.2 with > BioC 1.7. > > When I use mt.teststat(test="t") or mt.teststat(test="t.equalvar") I get > the > same results (which assumes EQUAL variances). See code below. > > Am I making some mistake or could there be a bug in the function? > > Ann > > ************************** > cl<-c(1,1,0,0,1,0) > test1<-mt.teststat(exprs(data),cl,test="t") > test2<-mt.teststat(exprs(data),cl,test="t.equalvar") > > test1[1:10] > # -1.7941959 -0.8467331 -1.0077421 -0.3012158 2.4909231 > test2[1:5] > # -1.7941959 -0.8467331 -1.0077421 -0.3012158 2.4909231 > > #Variances are NOT EQUAL: > var1.1<-var(exprs(data)[1,c(1:2,5)]) > var1.2<-var(exprs(data)[1,c(3:4,6)]) > var1.1 > # 43 > var1.2 > # 305.33 > > #Test statistic uses POOLED t-test: > mean1.1<-mean(exprs(data)[1,c(1:2,5)]) > mean1.2<-mean(exprs(data)[1,c(3:4,6)]) > sp.1<-sqrt( (2*var1.1 + 2*var1.2)/4 ) > t.1<- (mean1.1-mean1.2)/(sp.1*sqrt(2/3)) > t.1 > # -1.794196 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > -- 10 GB Mailbox, 100 FreeSMS/Monat http://www.gmx.net/de/go/topmail +++ GMX - die erste Adresse f?r Mail, Message, More +++