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Table 1 Results for two-study simulation data. True integration-driven discovery rate (t IDR) and true integration-driven revision rate (t IRR) for threshold value of posterior probability of differential expression γ = 0.95, and the number of true discovered genes for posterior expected false discovery rate pe FDR = 5%, for the Bayesian standardized expression integration (SEI) and probability integration (PI) models. Results are shown for the three levels of simulated percent differentially expressed genes p s and three levels of mean inter-study variability τ g 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacqWFepaDdaqhaaWcbaGaem4zaCgabaGaeGOmaidaaaaa@30EE@ for the two-study simulation data.

From: Bayesian meta-analysis models for microarray data: a comparative study

   p s = 5% p s = 10% p s = 25%
Two-Study Simulation Data SEI PI SEI PI SEI PI
Low: mean τ g 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacqWFepaDdaqhaaWcbaGaem4zaCgabaGaeGOmaidaaaaa@30EE@ = 0.1 (DE); 0.01 (non DE) t IDR, γ = 0.95 24.6% 29.9% 12.9% 18.9% 3.8% 9.0%
  t IRR, γ = 0.95 3.7% 0% 2.9% 1.4% 6.2% 1.5%
  True Genes, pe FDR = 5% 84 92 183 196 479 513
Medium: mean τ g 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacqWFepaDdaqhaaWcbaGaem4zaCgabaGaeGOmaidaaaaa@30EE@ = 0.3 (DE); 0.03 (non DE) t IDR, γ = 0.95 11.2% 19.5% 10.8% 16.2% 2.6% 6.4%
  t IRR, γ = 0.95 16.4% 7.5% 15.9% 4.5% 16.4% 3.1%
  True Genes, pe FDR = 5% 80 97 185 211 493 547
High: mean τ g 2 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacqWFepaDdaqhaaWcbaGaem4zaCgabaGaeGOmaidaaaaa@30EE@ = 0.7(DE); 0.07(non DE) t IDR, γ = 0.95 11.0% 15.3% 5.4% 7.6% 2.9% 4.9%
  t IRR, γ = 0.95 16.7% 7.7% 19.9% 6.6% 16.0% 4.8%
  True Genes, pe FDR = 5% 93 105 212 235 572 617
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BMC Bioinformatics

ISSN: 1471-2105

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