After performing highly sensitive acceleration measurements during two years of drag-free flight around the Earth, MICROSCOPE provided the best constraint on the Weak Equivalence Principle (WEP) to date. Beside being a technological challenge, this experiment required a specialised data analysis pipeline to look for a potential small signal buried in the noise, possibly plagued by instrumental defects, missing data and glitches. This paper describes the frequency-domain iterative least-square technique that we developed for MICROSCOPE. In particular, using numerical simulations, we prove that our estimator is unbiased and provides correct error bars. This paper therefore justifies the robustness of the WEP measurements given by MICROSCOPE.
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