-------- Original Message -------- Subject: PLS and significance test Date: Tue, 9 Dec 2008 05:37:40 -0800 (PST) From: Demetrios Halazonetis <[EMAIL PROTECTED]> To: <[email protected]> Hi, We are investigating integration in the craniofacial structures and running PLS analysis on configurations of landmarks. We have used tpsPLS, MorphoJ and IMP (PLSMaker). The problem is that although all three software report the same correlation coefficients between the two blocks of landmarks, the permutation tests give very different P values. Here is the output for a test sample of 30 specimens: tpsPLS: Number and percent of correlations >= observed: Dim. Observed Count Percent 1 0.726880 19 1.90% <---- 2 0.611517 108 10.80% 3 0.479918 544 54.40% 4 0.416872 707 70.70% 5 0.534085 99 9.90% 6 0.335551 814 81.40% MorphoJ: Singular values and pairwise correlations of PLS scores between blocks: Singular value P-value (perm.) % total covar. Correlation P-value (perm.) PLS1 0,00071285 0,0225 64,620 0,72709 0,4386 <----- PLS2 0,00040780 0,2129 21,148 0,61194 0,4380 PLS3 0,00023018 0,7320 6,738 0,47995 0,7328 PLS4 0,00017020 0,6327 3,684 0,41794 0,5551 PLS5 0,00016025 0,0441 3,266 0,53389 0,5594 PLS6 0,00006549 0,6783 0,545 0,33590 0,9852 IMP: For the correlations of the SVD scores correlation Exceedances p-value s1 0.7269 0 0.000 <---- s2 0.6115 0 0.000 s3 0.4799 0 0.000 s4 0.4169 0 0.000 s5 0.5341 0 0.000 s6 0.3356 0 0.000 As you can see, the correlation for dimension 1 is 0.727 in all three reports, but the P values (next to the arrows) are completely different (and do not vary much when different number of permutations are used). Any clues? Thanks, Demetris Halazonetis and Nikos Gkantidis Orthodontic Dept., Dental School, Athens University, Greece. -- Replies will be sent to the list. For more information visit http://www.morphometrics.org
