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