A method of controlling a polishing operation includes measuring a plurality of spectra at a plurality of different positions on a substrate to provide a plurality of measured spectra. For each measured spectrum of the plurality of measured spectra, a characterizing value is generated based on the measured spectrum. For each characterizing value, a goodness of fit of the measured spectrum to another spectrum used in generating the characterizing value is determined. A wafer-level characterizing value map is generated by applying a regression to the plurality of characterizing values with the plurality of goodnesses of fit used as weighting factors in the regression. A polishing endpoint or a polishing parameter of the polishing apparatus is adjusted based on the wafer-level characterizing map, and the substrate or a subsequent substrate is polished in the polishing apparatus with the adjusted polishing endpoint or polishing parameter.