The Primordial Inflation Explorer (PIXIE) is an Explorer-class mission concept to measure cosmological signals from both linear polarization of the cosmic microwave background and spectral distortions from a perfect blackbody. The targeted measurement sensitivity is 2--4 orders of magnitude below competing astrophysical foregrounds, placing stringent requirements on instrument calibration. An on-board blackbody calibrator presents a polarizing Fourier transform spectrometer with a known signal to enable conversion of the sampled interference fringe patterns from telemetry units to physical units. We describe the instrumentation and operations needed to calibrate PIXIE, derive the expected uncertainty for the intensity, polarization, and frequency scales, and show the effect of calibration uncertainty in the derived cosmological signals. In-flight calibration is expected to be accurate to a few parts in $10^6$ at frequencies dominated by the CMB, and a few parts in $10^4$ at higher frequencies dominated by the diffuse dust foreground.
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