Table 3.

True and estimated (posterior means) cQTL effects under the MD1 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 ${\eta }_{j,k}^I,$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
2	1	0	0	0	0	0	0	0	0	0
	2	0	0	0	0	0	0	0	0	0.26
	3	0	0	0	0	0	0	0	0	0
4	1	0	0	0	0	0	0	0	0	0
	2	0	0	0	0	0	0	6	5.96	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	−12.87	0	0	−1.46	0	0	7.14
	3	0	0	0	0	0	0	0	0	0
14	1	0	0	0	6	5.78	5.52	0	0	0
	2	0	0	−0.2	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	5.66	5.77	0	0	0
21	1	0	0	0	0	0	0	0	0	0
	2	0	0	0.26	0	0	0	0	0	0
	3	0	0	0	0	0	0	0	0	0
24	1	6	0.24	2.78	0	0	0	0	0	0
	2	6	1.09	3.40	0	0	0	0	0	0
	3	6	0.46	3.50	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.