Table 8.

True and estimated (posterior means) cQTL effects in the analysis of Trait 1 using the MD1 version of the HB single-trait cQTL model with (A) 10% markers and 10% expressions coded as missing and (B) 10% markers and 30% expressions coded as missing, and for s^l = 0.09.

Pair j	Size of the regulatory effects ${\text{η}}_{j,1}^I,$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) MD1 TRAIT 1, WITH 10%G, 10%E CODED AS MISSING
1	0	0	0	0	0	0
3	0	0.23	0	0	0	0
6	0	0	0	0	0	0
12	0	0	0	0	0	0
14	0	0	6	2.36	0	0
17	0	0.70	0	0	0	0
18	0	0.22	0	0	0	0
19	0	0	0	0	0	0
22	0	0	0	0	0	0.23
23	0	0	0	0	0	0.27
24	6	0.83	0	−0.45	0	0
(B) MD1 TRAIT 1, WITH 10%G, 30%E CODED AS MISSING
3	0	0.21	0	0	0	0
6	0	0	0	0	0	0
12	0	0	0	0	0	0
13	0	0	0	0	0	0
14	0	0	6	4.49	0	0
16	0	0	0	0	0	0
17	0	0.63	0	−0.26	0	0
18	0	0.22	0	0	0	0
19	0	0	0	0	0	0
22	0	0	0	0	0	0
23	0	0	0	0	0	0.20
24	6	0.71	0	−0.39	0	0