TRL Calibration reference plane - thru vs reflect.

According to HP Product Note 8510-5A:
"The phase reference can be specified by the Thru or Reflect during the TRL 2-PORT calibration. SET REF: THRU corresponds to a reference plane set by Thru standard (or the ratio of the physical lengths of the Thru and Line) and SET REF: REFLECT corresponds to the Reflect standard."

This option only matters when you are doing a TRL calibration, and it determines where the network analyzer's reference planes will be assigned; that is, the physical locations which are assigned to be the "test ports" of the network analyzer system. Where these are located will obviously effect the resulting measurements of your DUT (primarily it effects the phase angles of your measurements).

If your TRL calibration kit contains a zero-length THRU, then use this to set the reference planes. If the THRU has length, and this length is accurately known, then you can still use it. If your REFLECT standard is very well defined, like a precision short circuit, then you can use it to set the planes. The idea here is to choose whichever one will give you the more precise definition of the physical locations of your reference planes. For example, if your REFLECT standard were a microstrip open circuit, that would be a poor choice - probably better to use the THRU.