Table 9.

True and estimated (posterior means) cQTL effects in the analysis of Trait 1 using the MD2 version of the HB single-trait cQTL model with (A) 10% markers and 10% expressions coded as missing and (B) 10% markers and 30% missing expressions coded as missing, and for Bernoulli parameter s^l = 0.09.

Pair j	Size of the regulatory effects ${\eta }_{j,1}^I,$l = {M, E, ME}
	${\text{η}}_j^M$		${\text{η}}_j^E$		${\text{η}}_j^{\mathrm{ME}}$
	True value	Estimated	True value	Estimated	True value	Estimated
(A) MD2, TRAIT 1, 10% G, 10% E CODED AS MISSING
1	0	0	0	0	0	0
3	0	0.53	0	0	0	0
6	0	0.89	0	0	0	0
9	0	1.08	0	0	0	−0.46
12	0	0	0	0	0	0
14	0	0	6	1.57	0	0
15	0	0	0	0	0	0
16	0	0	0	0	0	0
17	0	0.66	0	0	0	0
18	0	0.39	0	0	0	0
21	0	0	0	0	0	0
22	0	0.22	0	0	0	0
24	6	2.40	0	0	0	0
(B) MD2, TRAIT 1, 10% G, 30% E CODED AS MISSING
1	0	0	0	0	0	0
3	0	0.50	0	0	0	0
6	0	0.33	0	0	0	0
9	0	2.03	0	0	0	0
12	0	0	0	0	0	0.23
13	0	0	0	0	0	0
14	0	0	6	4.64	0	0
15	0	0	0	0	0	0
16	0	−0.21	0	0	0	0
17	0	0.47	0	−0.32	0	0
18	0	0.28	0	0	0	0
19	0	0	0	0	0	0
22	0	0.24	0	0	0	0
24	6	2.72	0	0	0	0