Table 3.

Comparison of the inference results for the relative protein expression levels under different settings of variations. The true values are x₂ = −0.04, x₃ = −0.48, and x₄ = −0.66. “Bayesian” refers to our method. “ANOVA 1” considers the sample effect, peptide effect, experimental effect, and the interaction of sample and peptide effect. “ANOVA 2” removes the interaction term from the analysis of “ANOVA 1.” “Log-ratio” calculates the means of peptide log-ratios

			Bayesian			ANOVA 1
${\sigma }_x^2$	${\sigma }_z^2$	${\sigma }_{\epsilon }^2$	x̂2	x̂3	x̂4	x̂2	x̂3	x̂4
10−4	10−4	10−4	−0.037 (−0.06, −0.01)	−0.480 (−0.50, −0.46)	−0.662 (−0.69, −0.64)	−0.051 (−0.053, −0.048)	−0.484 (−0.487, −0.481)	−0.660 (−0.663, −0.657)
10−4	1	1	−0.044 (−0.23, 0.14)	−0.526 (−0.73, −0.33)	−0.613 (−0.80, −0.43)	0.100 (−0.13, 0.33)	−0.567 (−0.78, −0.35)	−0.529 (−0.75, −0.30)
10−2	0.1	1.5	−0.094 (−0.28, 0.09)	−0.593 (−0.79, −0.40)	−0.729 (−0.93, −0.52)	0.052 (−0.12, 0.22)	−0.589 (−0.77, −0.41)	−0.516 (−0.71, −0.32)
10−2	1	1.5	0.051 (−0.13, 0.23)	−0.279 (−0.46, −0.10)	−0.610 (−0.80, −0.42)	0.123 (−0.05, 0.30)	−0.218 (−0.40, −0.03)	−0.514 (−0.70, −0.33)
10−2	10	1.5	−0.023 (−0.24, 0.19)	−0.336 (−0.55, −0.12)	−0.608 (−0.83, −0.39)	−0.039 (−0.31, 0.23)	−0.272 (−0.54, −0.01)	−0.218 (−0.52, 0.08)
10−2	50	1.5	0.050 (−0.15, 0.25)	−0.403 (−0.60, −0.20)	−0.626 (−0.83, −0.42)	0.182 (−0.07, 0.43)	−0.146 (−0.40, 0.11)	−0.520 (−0.77, −0.27)
			ANOVA 2			Log-ratio
10−4	10−4	10−4	−0.051 (−0.053, −0.049)	−0.484 (−0.486, −0.482)	−0.658 (−0.661, −0.656)	−0.036	−0.480	−0.662
10−4	1	1	0.005 (−0.17, 0.18)	−0.575 (−0.75, −0.40)	−0.560 (−0.74, −0.38)	−0.098	−0.475	−0.533
10−2	0.1	1.5	0.025 (−0.14, 0.19)	−0.525 (−0.70, −0.35)	−0.506 (−0.68, −0.33)	0.046	−0.429	−0.427
10−2	1	1.5	0.094 (−0.08, 0.27)	−0.216 (−0.39, −0.04)	−0.488 (−0.67, −0.31)	−0.049	−0.343	−0.555
10−2	10	1.5	−0.028 (−0.28, 0.22)	−0.194 (−0.45, 0.06)	−0.144 (−0.41, 0.12)	0.232	−0.100	−0.321
10−2	50	1.5	0.130 (−0.10, 0.36)	−0.172 (−0.41, 0.07)	−0.553 (−0.79, −0.32)	0.048	−0.379	−0.610