The multiplicity problem in linkage analysis of gene expression data – the power of differentiating cis- and trans-acting regulators

Table 2 Results of using different distance criterion to define cis regulators

	3 Mb		10 Mb		20 Mb
Parameter	cis (<)	trans (≥)	cis (<)	trans (≥)	cis (<)	trans (≥)
No. tests	9,699	3,845,729	29,827	3,825,601	52,853	3,802,575
${\hat{π}}_{0}$ (%)	87.68	95.05	89.32	95.08	89.62	95.11
Framework I, α = 0.0001
No. rejections	69	7,974	204	7,839	302	7,741
$F \hat{D} R$ (%)	1.23	4.58	1.31	4.64	1.57	4.67
E [No. false positives]	1	365	3	363	5	361
Framework II, γ = 0.05
No. rejections	200	8,398	519	8,113	761	7,927
E [No. true positives]	190	7,978	493	7,707	723	7,531
Framework III, R = 2,000
Rejection without stratification	29	1971	90	1,910	127	1,873
Rejection with stratification	67	1933	184	1,816	222	1,778
Overall $F \hat{D} R$ (%)	2.03		1.99		1.99

ISSN: 1753-6561