Fig 5. Comparison of the log-average and Kalman filter approaches using N = 2 to N = 10 replicates simulated at (a) low (b) medium and (c) high noise levels under log-normal noise model.

RMS errors were calculated between ground truth and log-averaged reactivities (solid line) and between ground truth and the Kalman filtered reactivities (dotted line) over entire set of nucleotides. Error calculations were carried out in the log domain and the ground truth values were the log reactivities. See Methods for RMS calculation details. In low noise regimes, only a negligible difference between the log-averaging and Kalman filtering approaches is observed. However, in the higher noise regime, the Kalman filtering approach better recovers the ground truth. This advantage is marginal after the replicate count is increased beyond 4. Note that errors increase with increasing noise levels.