Table 7.

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 10% expressions coded as missing, and different values of s^l.

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	Estimated		True value	Estimated
		sl = 0.0033	sl = 0.013		sl = 0.0033	sl = 0.013		sl = 0.0033	sl = 0.013
(A) MD2, TRAIT 1, 10% G, 10% E CODED AS MISSING
3	0	0.21	0.30	0	0	0	0	0	0
6	0	0.28	0.41	0	0	0	0	0	0
9	0	0	0.26	0	0	0	0	0	0
14	0	0	0	6	0	0.46	0	0	0
17	0	0	0	0	0	0	0	0	0
18	0	0	0	0	0	0	0		0
24	6	1.55	2.40	0	0	0	0	0	0
(B) MD2, TRAIT 1, 10% G, 30% E CODED AS MISSING
3	0	0	0.23	0	0	0	0	0	0
6	0	0.24	0.20	0	0	0	0	0	0
9	0	0	0.39	0	0	0	0	0	0
14	0	0	0	6	0.63	2.58	0	0	0
17	0	0	0	0	0	0	0	0	0
24	6	1.38	2.38	0	−0.21	−0.23	0	0	0

A bold font is used to indicate positions where the true or estimated effect was non-zero. The shaded cells indicate false positives and false negatives.