Table 3.

MAR missing values

	MAE		RMSE
Method	M-value	B-value	M-value	B-value
(a) Healthy datasets
mean	0.041 ±0.001	0.040 ±0.001∗	0.073 ±0.002	0.070 ±0.001∗
impute.knn	0.043 ±0.004∗	0.061 ±0.009	0.082 ±0.009∗	0.110 ±0.015
softImpute	0.042 ±0.002∗	0.043 ±0.007	0.077 ±0.005	0.082 ±0.017∗
imputePCA	0.037 ±0.001	0.036 ±0.001∗	0.069 ±0.002	0.066 ±0.002∗
SVDmiss	0.043 ±0.001	0.036 ±0.001∗	0.079 ±0.003	0.067 ±0.002∗
missForest	0.035 ±0.001	0.035 ±0.001∗	0.064 ±0.002	0.061 ±0.002∗
methyLImp	0.037 ±0.001	0.033 ±0.001∗	0.068 ±0.002	0.063 ±0.002∗
(b) Disease datasets
mean	0.060 ±0.001	0.060 ±0.001∗	0.101 ±0.002	0.097 ±0.002∗
impute.knn	0.067 ±0.005∗	0.087 ±0.010	0.115 ±0.009∗	0.144 ±0.014
softImpute	0.062 ±0.003	0.065 ±0.011	0.106 ±0.006∗	0.116 ±0.026
imputePCA	0.054 ±0.001	0.053 ±0.001∗	0.095 ±0.002	0.090 ±0.002∗
SVDmiss	0.067 ±0.001	0.057 ±0.001∗	0.114 ±0.003	0.104 ±0.004∗
missForest	0.053 ±0.001	0.053 ±0.001∗	0.093 ±0.002	0.088 ±0.002∗
methyLImp	0.053 ±0.001	0.049 ±0.001∗	0.092 ±0.002	0.089 ±0.002∗

Average Mean Average Error (MAE) and Root Mean Square Error (RMSE) imputation performance ± standard deviation. For each method, the ^∗ symbol indicates the measure (either M-value or β-value) for which the Wilcoxon signed-rank test p-value is <0.05. Best results per metric with respect to the Wilcoxon signed-rank test are highlighted in bold