A transfer function is a total measurement of the amplitude and phase response of a device under test
A key part of an accurate transfer function is the removal of the input test signal response from the final measurement. This is done by passing a sample of the input signal to the second channel of the analyzer and removing its response from the response of the device under test.
You should use logarithmic amplitude scaling; subtracting two logarithmic quantities equates to division of their ratio values.
Connect a noise generator to the input of the device under test.
Connect the output of the device under test to one input channel of the analyzer.
Connect same signal generator to a different input channel of the analyzer.
Setup a Composite Channel to produce the transfer function between the two channels
Run the analyzer until the average spectrum response settles to a consistent level.
The spectrum display contains the amplitude response of the device and the phase display contains the phase response.