A method of controlling the polishing of a substrate includes polishing a substrate on a first platen using a first set of parameters, obtaining first and second sequences of measured spectra from first and second regions of the substrate with an in-situ optical monitoring system, generating first and second sequences of values from the first and second sequences of measured spectra, fitting first and second linear functions to the first and second sequences of values, determining a difference between the first linear function and the second linear function, adjusting at least one parameter of the first set of parameters based on the difference, and polishing the second substrate on the first platen using the adjusted parameter.