[R] PCA with not non-negative definite covariance

[hadley wickham]

> I suppose that another option could be just to use classical
> multi-dimensional scaling. By my understanding this is (if based on
> Euclidian measure) completely analogous to PCA, and because it's based
> explicitly on distances, I could easily exclude the variables with NA's on a
> pairwise basis when calculating the distances.

I don't think it as straightforward as that because distances
calculated on observations with missing values will be smaller than
other distances.  I suspect adjusting for this would be in some way
equivalent to imputation.

Exactly what do you want a low-dimensional representation of your data
set for?  (And why are you concerned about negative eigenvalues?)

Hadley