Methods of calibrating a fluid analyzer for use in a wellbore are described. An example method of generating calibration data for a fluid analyzer for use in a downhole tool involves lowering a downhole tool including a fluid analyzer to a location in a wellbore, measuring, via the fluid analyzer, a characteristic value of a calibration fluid or a vacuum while the fluid analyzer is at the location, obtaining an expected characteristic value for the calibration fluid or the vacuum at the location, and comparing the measured characteristic value to the expected characteristic value to generate a calibration value for the fluid.