This setting is used for setting the reference measurement that is used for performing complex division. It will only have an effect on the frequency domain plot types.
If the check box is checked, division will be performed.
The channel used for division must be selected, there are several options. In the example below, channel 2 is used for division when a 2-channel measurement is performed
Click the button to open the Plot->Plot Type Settings->General Frequency Domain… which contains all the settings for the reference measurement.