Correct calibration of reflection (S11) measurement
Yes what you are planning on doing is very common in RF measurements. You need to follow the well established process of 1 port calibration. You will need 3 calibration standards Open, Short and Load to determine the three error terms involved and eliminate them.
See this, page 12 specifically
http://emlab.uiuc.edu/ece451/appnotes/Rytting_NAModels.pdf