```Date: Mar 27, 2011 9:45 AM
Author: Tikkuhirvi Tietavainen
Subject: Procrustes factor analysis

Hello All,I'm trying to find a way how to use Factor analysis to improve the separation of two data sets that are measured from the same patients before and after a procedure. The sets both include 100 observations (patients) and seven variables that have two dimensions or factors. If I plot the two data sets first variable against second variable (without factor analysis), I can see a difference between the data sets. But how can I use factor analysis and the two factors (factor scores?) to compare the two data sets?I was advised to use something called the procrustes rotation to ensure that the two data sets have the same rotation and can be compared. I have never used it, but here's what I did:A1;%First data set, before procedure.A2;%Second data set, after procedure.[lambda1,psi1,T1,stats1,F1] = factoran(A1,2);%Default is varimax rotation.[lambda2,psi2,T2,stats2,F2] =factoran(A2,2,'rotate','procrustes','target',lambda1);figure;plot(F1(:,1),F1(:,2),'b.',F2(:,1),F2(:,2),'r+')It would seem that the distributions are as similar as possible. What am I missing here? Am I supposed to be comparing something else than the factor scores F1 and F2?Thank you,Aino
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