Can We Trust Score Plots?

In this paper, we discuss the validity of using score plots of component models such as partial least squares regression, especially when these models are used for building classification models, and models derived from partial least squares regression for discriminant analysis (PLS-DA). Using examples and simulations, it is shown that the currently accepted practice of showing score plots from calibration models may give misleading interpretations. It is suggested and shown that the problem can be solved by replacing the currently used calibrated score plots with cross-validated score plots.