A reference matrix contains valid measurements characterizing operation of a multivariate process (220). Modeling parameters of the reference matrix are derived (222-232). The final model parameters, balanced with respect to measuring and modeling uncertainties (232), are applied to model (204) a new set of measurements (200). If the new set has no faults (206) then all modeled values and modeling uncertainties (208) can be used to control the process (218). If the new set has only one fault (210) ten the modeled value and modeling uncertainty of the faulted measurement plus the measured values and measuring uncertainties of the unfaulted measurements (212) can be used to control the process (218) while repair procedures are implemented for the identified fault (216). If the new set has more than one fault (214) then the process (218) should be shut down, and repair procedures should be implemented (216) for all identified faults.