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I'm running a PCA using the R function prcomp. This is the function:

d2.pca <- prcomp(sel.d2,center = TRUE,scale. = TRUE)

So variables are scaled an centered (this always has to be done, right?).

This is my original loadings matrix:

                    PC1    PC2    PC3    PC4
var1              0.551 -0.246  0.576 -0.551
var2             -0.545 -0.233  0.736  0.328
var3             -0.427 -0.704 -0.333 -0.460
var4             -0.467  0.625  0.126 -0.613

When I apply variamx rotation:

varimax(d2.pca$rotation)

The output is this one:

$loadings

Loadings:
                 PC1 PC2 PC3 PC4
var1              1             
var2                      1     
var3                 -1         
var4                         -1 

                PC1  PC2  PC3  PC4
SS loadings    1.00 1.00 1.00 1.00
Proportion Var 0.25 0.25 0.25 0.25
Cumulative Var 0.25 0.50 0.75 1.00

$rotmat
       [,1]  [,2]   [,3]   [,4]
[1,]  0.551 0.427 -0.545  0.466
[2,] -0.246 0.704 -0.232 -0.625
[3,]  0.576 0.333  0.736 -0.125
[4,] -0.551 0.461  0.328  0.613

This looks very strange for me, how should I interpret the loadings ("1" and "-1" values) matrix after varimax rotation? Any help or advise will be appreciated, I'm probably missing something...

Note: KMO was 0.6 for the correlation matrix. Just in case, here it is the correlation matrix:

         var1        var2        var3        var4
var1    1.000      -0.680      -0.491      -0.771
var2   -0.680       1.000       0.697       0.550
var3   -0.491       0.697       1.000       0.166
var4   -0.771       0.550       0.166       1.000 
David VR
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  • This doesn't sound like a specific programming question; it sounds like a question about PCA and varimax which are statistical methods. This question seems like a better fit for [stats.se] instead. – MrFlick Oct 16 '14 at 18:02
  • Just posted it in Cross Validated. Thanks for the comment – David VR Oct 17 '14 at 07:08

0 Answers0