Table 2.

True and estimated (posterior means) cQTL effects under the MD1 version of the HB multi-trait cQTL model with 10% markers and 10% 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 value	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	4.01	4.11
	3	0	0	0	0	0	0	0	0	0
14	1	0	0	0	6	5.52	5.53	0	0	0
	2	0	0	0	0	0	0	0	0	0
	3	0	0	0	0	0	0	0	0	0
16	1	0	0	0	0	0	0	0	0	0
	2	0	0	−0.27	0	0	0	0	0	0
	3	0	0	0	0	0	0	0	0	0
18	1	0	0	0	0	0	0	0	0	0
	2	0	0	0	0	0	0	0	0	0
	3	0	0	0	6	5.95	5.95	0	0	0
22	1	0	0	0	0	0	0	0	0	0
	2	0	0	0	0	0	0	0	0.65	0.63
	3	0	0	0	0	0	0	0		0
24	1	6	5.05	5.20	0	0	0	0	0	0
	2	6	5.57	5.68	0	0	0	0	0	0
	3	6	5.25	5.36	0	0	0	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.