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RF Hints
I used 10dB attenuators on the transmit output port and receive port, in order to provide a reasonable broadband match to the Device Under Test, because the Lime's match varies. This makes noise worse of course. It would be better with 6dB attenuators but I didn't have any good ones with the SMA connectors that I used for my Lime.
For the Lime-USB, use the low-band receive port below 1.5GHz and the high band port above. Use Transmit port 2 above 2.1GHz because it produces more power. The limitation seems to be crosstalk between transmit and receive ports, and low output from the transmitter ports at high frequencies (3GHz) where noise dominates measurements about 15dB below calibration.
If LNA and PGA gain are at maximum and RSSI during calibration does not reach around 50,000, either the wrong ports are being used or the transmit power is low at that frequency. Try a measurement with no device connected to see what the response is like - anything you see is the noise floor.