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Table 1 Summary statistics and results under the three frameworks

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

   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