A solution for reducing interference in noninvasive spectroscopic measurements of tissue and blood analytes is provided. By applying a basis set representing various tissue components to a collected sample measurement, measurement interferences resulting from the heterogeneity of tissue, sampling site differences, patient-to-patient variation, physiological variation, and instrumental differences are reduced. Consequently, the transformed sample measurements are more suitable for developing calibrations that are robust with respect to sample-to-sample variation, variation through time, and instrument related differences. In the calibration phase, data associated with a particular tissue sample site is corrected using a selected subset of data within the same data set. This method reduces the complexity of the data and reduces the intra-subject, inter-subject, and inter-instrument variations by removing interference specific to the respective data subset. In the measurement phase, the basis set correction is applied using a minimal number of initial samples collected from the sample site(s) where future samples will be collected.