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. 2019 Sep 16;106(4):823–840. doi: 10.1093/biomet/asz037

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© 2019 Biometrika Trust

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

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Fig. 1. — The false discovery proportion, FDP, for each method at a -value threshold of 0.2 in simulations when (a) and (b) . BC is our shrinkage-corrected method defined in Algorithm 2 and is the number of factors used to estimate . CATE-RR, dSVA, IRW-SVA, RUV-2 and RUV-4 are the methods proposed in Leek & Storey (2008), Gagnon-Bartsch & Speed (2012), Gagnon-Bartsch et al. (2013), Lee et al. (2017) and Wang et al. (2017), respectively. These five methods were all applied with . Inference with None was performed using the design matrix .

Inline graphic — The false discovery proportion, FDP, for each method at a -value threshold of 0.2 in simulations when (a) and (b) . BC is our shrinkage-corrected method defined in Algorithm 2 and is the number of factors used to estimate . CATE-RR, dSVA, IRW-SVA, RUV-2 and RUV-4 are the methods proposed in Leek & Storey (2008), Gagnon-Bartsch & Speed (2012), Gagnon-Bartsch et al. (2013), Lee et al. (2017) and Wang et al. (2017), respectively. These five methods were all applied with . Inference with None was performed using the design matrix .