A method for calibrating measurement or analysis systems that is externally traceable, simple, and repeatable, which is particularly amenable to computer control, and a unique programmable phase-gain amplifier which is especially suited for use in the calibration method, are disclosed. Alternatively, a programmable sample clock delay technique is disclosed to provide phase calibration. The method employs an externally traceable digital voltmeter to measure the magnitude of the signal being applied to an input channel of the measurement system; and obtains a digital representation of the output of the channel. When the input magnitude does not match the output magnitude, the programmable phase-gain amplifier gain is adjusted. These adjustments are made for each range of each channel. Thereafter, the relative phase shifts between channels is determined and the gain of a variable gain amplifier in the programmable phase-gain amplifier for each channel is changed to adjust the phase shift through each channel to the desired amount.