Table 5.

True and estimated (posterior means) cQTL effects under the MD2 version of the HB multi-trait cQTL model with 10% markers and 30% expressions coded as missing and different values of Bernoulli parameter s^l.

Location (j, k) of the effect ηj,k		Size of the regulatory effects ${\text{η}}_{j,k}^I,$l = {M, E, ME}
Pair j	Trait k	${\text{η}}_j^M$			${\text{η}}_j^E$			${\text{η}}_j^{\mathrm{ME}}$
		True value	Estimated		True	Estimated		True value	Estimated
			sl = 0.013	sl = 0.09		sl = 0.013	sl = 0.09		sl = 0.013	sl = 0.09
4	1	0	0	0	0	0	0	0	0	0
	2	0	0	0	0	0	0	6	0	0
	3	0	0	0	0	0	0	0	0	0
9	1	0	0	0	0	0	0	0	0	0
	2	0	0	0	0	0	0.31	0	0	0
	3	0	0	0	0	0	0	0	0	0
14	1	0	0	0	6	5.49	5.42	0	0	0
	2	0	0	0	0	0	0	0	0	0
	3	0	0	0	0	0	0	0	0	0
18	1	0	0	0.49	0	0	0	0	0	0
	2	0	0	0	0	0	0	0	0	0
	3	0	0	0	6	5.60	5.48	0	0	0
19	1	0	0	0	0	0	0	0	0	0
	2	0	0	0	0	0	0	0	0	−0.52
	3	0	0	0	0	0	0	0	0	0
22	1	0	0	0	0	0	0	0	0	0
	2	0	0	0	0	0	0	0	1.88	0
	3	0	0	0	0	0	0	0	0	0
24	1	6	0	1.21	0	0	−0.47	0	0	0
	2	6	0	0.20	0	0	−1.02	0	0	7.61
	3	6	0.2	1.09	0	0	−0.55	0	0	0

A bold font is used to indicate positions where the true or estimated effect was non-zero $\left(\left|{\overline{\eta }}_{j,k}^l\right|\ge 0.2\right).$ The shaded cells indicate false positives and false negatives.