[R] Scaling in predict.prcomp

Gad Abraham gabraham at csse.unimelb.edu.au
Sun Apr 20 08:36:51 CEST 2008


Say x.train is a matrix of covariates that I want to do PCA on, so I can 
do regression on its principal components, and x.test is a test set of 
the same covariates on which I want to evaluate the regression fit. I 
would like the covariates to be centred and scaled:

p <- prcomp(x.train, center=TRUE, scale=TRUE)
x.train.pc <- predict(p)

Now I want to get the PCs from the test set. Should I use the same 
center and scale vectors from the training set:

x.test.pc <- predict(p, newdata=x.test, center=p$center, scale=p$center)

or use the training set's own centers and scales:

x.test.pc <- predict(p, newdata=x.test, center=TRUE, scale=TRUE)


Gad Abraham
Dept. CSSE and NICTA
The University of Melbourne
Parkville 3010, Victoria, Australia
email: gabraham at csse.unimelb.edu.au
web: http://www.csse.unimelb.edu.au/~gabraham

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