1. A method for controlling a manufacturing apparatus, the method comprising the steps of: (a) identifying at least one input, the at least one input causing a change in at least two of a plurality of outputs; (b) storing values of the identified inputs and corresponding empirical output values along with predicted output values, wherein the predicted output values are calculated based on, in part, the values of the identified inputs; (c) calculating a set of transform coefficients by minimizing a score equation that is a function of, in part, differences between one or more of the empirical output values and their corresponding predicted output values, wherein the score equation is: 3 S p = &Sum; i, k &it; W i, k &af; ( y actual i &it; &it; k - y predicted i &it; &it; k &af; ( X &RightArrow; i ′ &af; ( X &RightArrow; i, P &RightArrow; ) ) ) 2 where: i—number of wafer; k—number of output; y actual —an empirical output value; y predicted —a predicted output value, as calculated based on transformed inputs for a particular wafer i ({right arrow over (X)} ′i ) {right arrow over (X)} ′i &equals;({right arrow over (X)} 1 ′i,X 2 ′i,X 3 ′i ) is transformed input values in a vector format; {right arrow over (X)} i &equals;(X 1 i,X 2 i,X 3 i ) for wafer i together with the transformation parameters {right arrow over (P)}, to thereby calculate an optimal value of {right arrow over (P)}; and (d) calculating one or more input values for one or more desired output values based on, in part, the calculated set of transform coefficients.