Hi,I am puzzled with different results in R, compared to SPSS and Senstools.Net. After running a PCA on the three software (for R, I use the PCA function programmed on the FactoMineR package), I extracted the loadings. In the three cases, the loadings are exactly identical.Then, I applied the varimax rotation on these loadings, and unfortunately, the results differ. A quick look at the resulting rotation matrix (rotmat) shows me, that the results are "sorted" differently. Here are my results for the rotation matrix:On R: > complet.varimax <- varimax(complet.loadings,normalize=T)$rotmat> complet.varimax      [,1]    [,2]    [,3]    [,4]   [,5]   [,6]   [,7]   [,8][1,]  0.529  -0.034  -0.411  -0.428  0.013 -0.297 -0.399  0.344[2,] -0.119   0.715  -0.194  -0.058  0.517 -0.219 -0.068 -0.337[3,]  0.081   0.087   0.722  -0.017  0.250 -0.472  0.092  0.413[4,]  0.110   0.039  -0.172   0.860  0.139 -0.013 -0.343  0.284[5,] -0.159  -0.353  -0.419   0.010  0.502 -0.114  0.578  0.275[6,] -0.122  -0.065   0.184  -0.240  0.502  0.670 -0.357  0.248[7,]  0.612   0.409   0.026   0.070 -0.061  0.420  0.497  0.159[8,] -0.522   0.427  -0.181  -0.107 -0.379  0.043  0.042  0.595On SPSS and Senstools.Net:Rotation     dim 1    dim 2    dim 3    dim 4    dim 5    dim 6    dim 7    dim 8dim 1        -0,53    -0,41    -0,43    -0,40     0,03    -0,34    -0,30    -0,01dim 2         0,12    -0,19    -0,06    -0,07    -0,71     0,34    -0,22    -0,52dim 3        -0,08     0,72    -0,02     0,09    -0,09    -0,41    -0,47    -0,25dim 4        -0,11    -0,17     0,86    -0,34    -0,04    -0,28    -0,01    -0,14dim 5         0,16    -0,42     0,01     0,58     0,35    -0,27    -0,11    -0,50dim 6         0,12     0,18    -0,24    -0,36     0,07    -0,25     0,67    -0,50dim 7         0,61    -0,03    -0,07    -0,50     0,41     0,16    -0,42    -0,06dim 8        -0,52     0,18     0,11    -0,04     0,43     0,60    -0,04    -0,38 Here, we can clearly see, that the results are similar, but sorted differently (in R, the second column correspond to the 5th column in SPSS or Senstools.Net).Concerning the loadings after rotation, the results are different to (permutation are seen too).Please, could someone explain me what's happening?Personally, I have the feeling that the results differ...is it true? Which results should I trust?Should you need any further information for answering me, do not hesitate to contact me (thierryworch@hotmail.com).I look forward to your response.Best regards, WORCH Thierry
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