How to interpret the S21 phase measured by LCA or VNA?
What do you mean by &quot;the reference to DC&quot;? It's the phase relative to the calibration of your Vector Network Analyzer, usually through/open/short/load. If properly calibrated, the S21 reads 0 dB at 0 degrees across the band if you connect the measurement coaxial cables directly together (eg: by connecting them with the &quot;through&quot; calibration standard).
Provided you are properly calibrated, the S21 value at each frequency corresponds to the phase shift and amplitude change of a sinusoidal signal passing through the device at that frequency. A positive phase value for S21 means that the output phase leads the input phase, and a negative value means the output phase lags the input phase (see also this question and answer).