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Table 1 Test statistics and quality measures. For the quality-based tests, the summarized quality measure, across treatment groups, is defined by Q g = maxw∈{1...W} R g w MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGsbGudaqhaaWcbaGaem4zaCgabaGaem4DaChaaaaa@30D4@ .

From: Tests for differential gene expression using weights in oligonucleotide microarray experiments

Quality Measures

Array specific measure

Group-specific measure R g w MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGsbGudaqhaaWcbaGaem4zaCgabaGaem4DaChaaaaa@30D4@

Notes

Q g 0 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGrbqudaqhaaWcbaGaem4zaCgabaGaeGimaadaaaaa@3049@

1.0

1.0

No filtering

Q g c a l l MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGrbqudaqhaaWcbaGaem4zaCgabaGaem4yamMaemyyaeMaemiBaWMaemiBaWgaaaaa@34B7@

q g i w * = { 1 i f c a l l i s P 0 o t h e r w i s e MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGXbqCdaqhaaWcbaGaem4zaCMaemyAaKMaem4DaChabaGaeiOkaOcaaOGaeyypa0ZaaiqaaeaafaqabeGacaaabaGaeGymaedabaGaemyAaKMaemOzayMaaGPaVlabdogaJjabdggaHjabdYgaSjabdYgaSjaaykW7cqWGPbqAcqWGZbWCcaaMc8UaemiuaafabaGaeGimaadabaGaem4Ba8MaemiDaqNaemiAaGMaemyzauMaemOCaiNaem4DaCNaemyAaKMaem4CamNaemyzaugaaaGaay5Eaaaaaa@5486@

min i ∈ { 1 … I } q g i w * MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacyGGTbqBcqGGPbqAcqGGUbGBdaWgaaWcbaGaemyAaKMaeyicI4Saei4EaSNaeGymaeJaeSOjGSKaemysaKKaeiyFa0habeaakiabdghaXnaaDaaaleaacqWGNbWzcqWGPbqAcqWG3bWDaeaacqGGQaGkaaaaaa@40AD@

All arrays must have present call to be included

Q g m e a n p MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGrbqudaqhaaWcbaGaem4zaCgabaGaemyBa0MaemyzauMaemyyaeMaemOBa4MaemiCaahaaaaa@362A@

q giw = detection p-value

1 − q ¯ g w = 1 − ∑ i ∈ w ( q g i w ) / n w MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqaIXaqmcqGHsislcuWGXbqCgaqeamaaBaaaleaacqWGNbWzcqWG3bWDaeqaaOGaeyypa0JaeGymaeJaeyOeI0YaaabuaeaacqGGOaakcqWGXbqCdaWgaaWcbaGaem4zaCMaemyAaKMaem4DaChabeaakiabcMcaPiabc+caViabd6gaUnaaBaaaleaacqWG3bWDaeqaaaqaaiabdMgaPjabgIGiolabdEha3bqab0GaeyyeIuoaaaa@47CB@

n w is the number of arrays in group w

Q g exp MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGrbqudaqhaaWcbaGaem4zaCgabaGagiyzauMaeiiEaGNaeiiCaahaaaaa@338F@

q giw = detection p-value

exp ⌊ λ ^ g w log ν ⌋ MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacyGGLbqzcqGG4baEcqGGWbaCdaGbdaqaaGGaciqb=T7aSzaajaWaaSbaaSqaaiabdEgaNjabdEha3bqabaGccyGGSbaBcqGGVbWBcqGGNbWzcqWF9oGBaiaawcp+caGL7Jpaaaa@4098@ for sensitivity parameter ν

λ ^ g w = − n w / ∑ i ∈ w log ( q g i w ) MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacuaH7oaBgaqcamaaBaaaleaacqWGNbWzcqWG3bWDaeqaaOGaeyypa0JaeyOeI0IaemOBa42aaSbaaSqaaiabdEha3bqabaGccqGGVaWldaaeqbqaaiGbcYgaSjabc+gaVjabcEgaNbWcbaGaemyAaKMaeyicI4Saem4DaChabeqdcqGHris5aOGaeiikaGIaemyCae3aaSbaaSqaaiabdEgaNjabdMgaPjabdEha3bqabaGccqGGPaqkaaa@497C@

Q g b e t a MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGrbqudaqhaaWcbaGaem4zaCgabaGaemOyaiMaemyzauMaemiDaqNaemyyaegaaaaa@34B7@

q giw = detection p-value

ν a ^ g w MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacqWF9oGBdaahaaWcbeqaaiqbdggaHzaajaWaaSbaaWqaaiabdEgaNjabdEha3bqabaaaaaaa@32EE@

a ^ g w = q ¯ g w / ( 1 − q ¯ g w ) MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacuWGHbqygaqcamaaBaaaleaacqWGNbWzcqWG3bWDaeqaaOGaeyypa0JafmyCaeNbaebadaWgaaWcbaGaem4zaCMaem4DaChabeaakiabc+caViabcIcaOiabigdaXiabgkHiTiqbdghaXzaaraWaaSbaaSqaaiabdEgaNjabdEha3bqabaGccqGGPaqkaaa@3F94@

Q g w e MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGrbqudaqhaaWcbaGaem4zaCgabaGaem4DaCNaemyzaugaaaaa@3225@

q giw = detection p-value

N/A

Weighted means x ¯ g w MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacuWG4baEgaqeamaaBaaaleaacqWGNbWzcqWG3bWDaeqaaaaa@3137@ and weighted standard deviations S gw

Q g L P E MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaacqWGrbqudaqhaaWcbaGaem4zaCgabaGaemitaWKaemiuaaLaemyraueaaaaa@32B8@

N/A

N/A

Local pooled error test [18]