Correlation of Principal Component Scores after Varimax Rotation

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Peter
Peter 2014-5-26
Hi all:
I'm extracting principal components from time series data and use the varimax rotation to interpret the PCs. In addition, I'd like to compute the rotated scores and use them for further analysis. However, the rotated scores are not uncorrelated anymore, although they should (I think) because the rotation matrix is orthornomal.
Here's a simple example in which I pick two PCs:
load hald [C,S] = pca(zscore(ingredients));
[L,T] = rotatefactors(C(:,1:2)); % L = C(:,1:2)*T
cov(S(:,1:2)*T)
Can anybody help?
Peter

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