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

Table 1 Summary statistics and results under the three frameworks

		Stratum
Parameter	Aggregated	cis	trans
Summary statistics
No. tests	3,855,428	16,018	3,839,410
$π^0 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacuWFapaCgaqcamaaBaaaleaacqaIWaamaeqaaaaa@2F9A@$ (%)	95.03	88.18	95.06
Minimal q-value	2.23 × 10^-7	1.12 × 10^-9	4.44 × 10^-7
Framework I, α = 0.0001
No. rejections	8,043	129	7,914
$F D^R MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGgbGrcuWGebargaqcaiabdkfasbaa@300F@$ (%)	4.56	1.09	4.61
E [No. false positives]	366	1	365
Framework II, γ = 0.05
No. rejections	8,541	339	8,262
E [No. true positives]	8,114	322	7,849
Framework III, R = 2,000
Rejection without stratification	2000	55	1945
Rejection with stratification	2000	133	1867
Overall $F D^R MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGgbGrcuWGebargaqcaiabdkfasbaa@300F@$ (%)	2.05	2.00