Systems and method for automatically determining offset correction values in a differential measurement system, and for correcting measurement offsets between two measurement devices in the differential measurement system. A method for determining real-time offset corrections in a gas analysis system having first and second gas analyzers includes for each of a plurality of gas concentrations within a range of gas concentrations: a) supplying the concentration of gas to the first and second gas analyzers through first and second gas flow lines, respectively; b) measuring a first gas concentration value using the first gas analyzer; and c) measuring a second gas concentration value using the second gas analyzer. The method may also include determining an offset value between each corresponding first and second gas concentration value, and determining a functional relationship between the offset values and gas concentration measurements of the first gas analyzer.