Table 2. Root Mean Squared Error from the Dilution Experiment.

Accuracy of different missing data methods found in our dilution experiment. The square root of the mean of squared errors, across all proteins, of log base 2 fold changes are presented for seven different methods of analysis. Results are shown separately for proteins with estimable and inestimable relative abundance contrasts.

	SVD	KNN	pMin	cMin	SMP	MM	2-Way
Estimable	1.72	2.28	1.43	2.08	0.94	1.13	1.19
Inestimable	4.39	5.48	3.51	3.48	3.30	NA	NA