We verified that these estimates were generally close to the values of (τ̂) obtained by optimization of the SCNA-fit likelihood (RMSE=0.26, Supplementary Fig. 12a). However, we noted a relationship between the level of discordance between ploidy estimators and the mean of the calibrated data (Supplementary Fig. 12b). Noting that correctly calibrated copy-ratio data always has mean = 1, we examined whether the miscalibration was due to scaling bias in the data. We found that this model explained nearly two thirds of the discordance between the two estimates (corrected RMSE=0.09, Supplementary Fig. 12c), by which we inferred that scaling biases dominated our miscalibration. This is significant, as such biases do not effect the estimation of tumor purity (Supplementary Fig. 12).
