I am using the function mt.teststat from the multtest package, version 1.0, date 2002-04-16, as bundled with R1.5.1 for Mac OSX/X11. The function mt.teststat(..., test="pairt") insists that the argument classlabel specify a sequence of (0,1) pairs, but seems to assume a consistent 0,1 order within those pairs, irrespective of the setting of classlabel. > xy <- matrix(c(12,15,13,16,17,19,3,8,5,13,16,12),byrow=T,ncol=6) > xy [,1] [,2] [,3] [,4] [,5] [,6] [1,] 12 15 13 16 17 19 [2,] 3 8 5 13 16 12 > > mt.teststat(xy, classlabel=rep(0:1,3), test="pairt") [1] 8.0000000 0.8320503 > apply(xy, 1, function(x)t.test(x[c(1,3,5)], x[c(2,4,6)],paired=T)$statistic) [1] -8.0000000 -0.8320503 > > mt.teststat(xy, classlabel=c(0,1,1,0,0,1), test="pairt") [1] 8.0000000 0.8320503 > apply(xy, 1, function(x)t.test(x[c(1,4,5)], x[c(2,3,6)],paired=T)$statistic) [1] -0.3592106 0.6069770 By contrast the setting test="blockf" does take notice of classlabel: > mt.teststat(xy, classlabel=rep(0:1,3), test="blockf") [1] 64.0000000 0.6923077 > apply(xy, 1, function(x)t.test(x[c(1,3,5)], >x[c(2,4,6)],paired=T)$statistic)^2 [1] 64.0000000 0.6923077 > > mt.teststat(xy, classlabel=c(0,1,1,0,0,1), test="blockf") [1] 0.1290323 0.3684211 > apply(xy, 1, function(x)t.test(x[c(1,4,5)], >x[c(2,3,6)],paired=T)$statistic)^2 [1] 0.1290323 0.3684211 Thus, it seems possible to get the correct t-statistics by taking the square root of the block F-statistic, and attaching the correct sign to it! John Maindonald. -- John Maindonald email: john.maindonald@anu.edu.au phone : +61 2 (6125)3473 fax : +61 2(6125)5549 Centre for Bioinformation Science, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200.