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Large-Scale Simultaneous Hypothesis Testing: The Choice of a Null Hypothesis

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Cited by:

  1. van Wieringen, Wessel N. & Stam, Koen A. & Peeters, Carel F.W. & van de Wiel, Mark A., 2020. "Updating of the Gaussian graphical model through targeted penalized estimation," Journal of Multivariate Analysis, Elsevier, vol. 178(C).
  2. Jian Zhang & Faming Liang, 2008. "Convergence of stochastic approximation algorithms under irregular conditions," Statistica Neerlandica, Netherlands Society for Statistics and Operations Research, vol. 62(3), pages 393-403, August.
  3. Raphael Gottardo & Adrian E. Raftery & Ka Yee Yeung & Roger E. Bumgarner, 2006. "Bayesian Robust Inference for Differential Gene Expression in Microarrays with Multiple Samples," Biometrics, The International Biometric Society, vol. 62(1), pages 10-18, March.
  4. Cheng, Cheng, 2009. "Internal validation inferences of significant genomic features in genome-wide screening," Computational Statistics & Data Analysis, Elsevier, vol. 53(3), pages 788-800, January.
  5. Sinjini Sikdar & Somnath Datta & Susmita Datta, 2017. "EAMA: Empirically adjusted meta-analysis for large-scale simultaneous hypothesis testing in genomic experiments," PLOS ONE, Public Library of Science, vol. 12(10), pages 1-19, October.
  6. Habiger, Joshua D. & Peña, Edsel A., 2014. "Compound p-value statistics for multiple testing procedures," Journal of Multivariate Analysis, Elsevier, vol. 126(C), pages 153-166.
  7. Pallavi Basu & Luella Fu & Alessio Saretto & Wenguang Sun, 2021. "Empirical Bayes Control of the False Discovery Exceedance," Working Papers 2115, Federal Reserve Bank of Dallas.
  8. Pei Fen Kuan & Derek Y. Chiang, 2012. "Integrating Prior Knowledge in Multiple Testing under Dependence with Applications to Detecting Differential DNA Methylation," Biometrics, The International Biometric Society, vol. 68(3), pages 774-783, September.
  9. Khalili, Abbas & Huang, Tim & Lin, Shili, 2009. "A robust unified approach to analyzing methylation and gene expression data," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1701-1710, March.
  10. David Amar & Ron Shamir & Daniel Yekutieli, 2017. "Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate," PLOS Computational Biology, Public Library of Science, vol. 13(8), pages 1-22, August.
  11. Pounds Stanley B. & Gao Cuilan L. & Zhang Hui, 2012. "Empirical Bayesian Selection of Hypothesis Testing Procedures for Analysis of Sequence Count Expression Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(5), pages 1-32, October.
  12. Ian W. McKeague & Min Qian, 2015. "An Adaptive Resampling Test for Detecting the Presence of Significant Predictors," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 110(512), pages 1422-1433, December.
  13. Lim Johan & Kim Jayoun & Kim Sang-cheol & Yu Donghyeon & Kim Kyunga & Kim Byung Soo, 2012. "Detection of Differentially Expressed Gene Sets in a Partially Paired Microarray Data Set," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(3), pages 1-30, February.
  14. Jian Zhang & Faming Liang, 2010. "Robust Clustering Using Exponential Power Mixtures," Biometrics, The International Biometric Society, vol. 66(4), pages 1078-1086, December.
  15. Fan, Jianqing & Hall, Peter & Yao, Qiwei, 2007. "To How Many Simultaneous Hypothesis Tests Can Normal, Student's t or Bootstrap Calibration Be Applied?," Journal of the American Statistical Association, American Statistical Association, vol. 102, pages 1282-1288, December.
  16. Chang Yu & Daniel Zelterman, 2020. "Distributions associated with simultaneous multiple hypothesis testing," Journal of Statistical Distributions and Applications, Springer, vol. 7(1), pages 1-17, December.
  17. Woo, Chi-Keung & Horowitz, Ira & Olson, Arne & Horii, Brian & Baskette, Carmen, 2006. "Efficient frontiers for electricity procurement by an LDC with multiple purchase options," Omega, Elsevier, vol. 34(1), pages 70-80, January.
  18. Hai Shu & Bin Nan & Robert Koeppe, 2015. "Multiple testing for neuroimaging via hidden Markov random field," Biometrics, The International Biometric Society, vol. 71(3), pages 741-750, September.
  19. Yong Wang, 2009. "The constrained Fisher scoring method for maximum likelihood computation of a nonparametric mixing distribution," Computational Statistics, Springer, vol. 24(1), pages 67-81, February.
  20. Bilgrau, Anders Ellern & Eriksen, Poul Svante & Rasmussen, Jakob Gulddahl & Johnsen, Hans Erik & Dybkaer, Karen & Boegsted, Martin, 2016. "GMCM: Unsupervised Clustering and Meta-Analysis Using Gaussian Mixture Copula Models," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 70(i02).
  21. Dachuan Shih & Seoung Kim & Victoria Chen & Jay Rosenberger & Venkata Pilla, 2014. "Efficient computer experiment-based optimization through variable selection," Annals of Operations Research, Springer, vol. 216(1), pages 287-305, May.
  22. Mark Hoekstra & CarlyWill Sloan, 2022. "Does Race Matter for Police Use of Force? Evidence from 911 Calls," American Economic Review, American Economic Association, vol. 112(3), pages 827-860, March.
  23. Wesley Tansey & Yixin Wang & Raul Rabadan & David Blei, 2020. "Double Empirical Bayes Testing," International Statistical Review, International Statistical Institute, vol. 88(S1), pages 91-113, December.
  24. Gary L Gadbury & Qinfang Xiang & Lin Yang & Stephen Barnes & Grier P Page & David B Allison, 2008. "Evaluating Statistical Methods Using Plasmode Data Sets in the Age of Massive Public Databases: An Illustration Using False Discovery Rates," PLOS Genetics, Public Library of Science, vol. 4(6), pages 1-8, June.
  25. Min Jin Ha & Wei Sun, 2014. "Partial correlation matrix estimation using ridge penalty followed by thresholding and re-estimation," Biometrics, The International Biometric Society, vol. 70(3), pages 762-770, September.
  26. Tianwei Yu, 2018. "A new dynamic correlation algorithm reveals novel functional aspects in single cell and bulk RNA-seq data," PLOS Computational Biology, Public Library of Science, vol. 14(8), pages 1-22, August.
  27. Kasa, Siva Rajesh & Rajan, Vaibhav, 2022. "Improved Inference of Gaussian Mixture Copula Model for Clustering and Reproducibility Analysis using Automatic Differentiation," Econometrics and Statistics, Elsevier, vol. 22(C), pages 67-97.
  28. Ryan Martin, 2021. "A Survey of Nonparametric Mixing Density Estimation via the Predictive Recursion Algorithm," Sankhya B: The Indian Journal of Statistics, Springer;Indian Statistical Institute, vol. 83(1), pages 97-121, May.
  29. Angela Schörgendorfer & Adam J. Branscum & Timothy E. Hanson, 2013. "A Bayesian Goodness of Fit Test and Semiparametric Generalization of Logistic Regression with Measurement Data," Biometrics, The International Biometric Society, vol. 69(2), pages 508-519, June.
  30. Ruggieri, Eric & Lawrence, Charles E., 2012. "On efficient calculations for Bayesian variable selection," Computational Statistics & Data Analysis, Elsevier, vol. 56(6), pages 1319-1332.
  31. Youngjo Lee & Jan F. Bjørnstad, 2013. "Extended likelihood approach to large-scale multiple testing," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 75(3), pages 553-575, June.
  32. David R. Bickel, 2011. "Estimating the Null Distribution to Adjust Observed Confidence Levels for Genome-Scale Screening," Biometrics, The International Biometric Society, vol. 67(2), pages 363-370, June.
  33. Campbell R. Harvey & Yan Liu & Heqing Zhu, 2014. ". . . and the Cross-Section of Expected Returns," NBER Working Papers 20592, National Bureau of Economic Research, Inc.
  34. Shigeyuki Matsui & Hisashi Noma, 2011. "Estimating Effect Sizes of Differentially Expressed Genes for Power and Sample-Size Assessments in Microarray Experiments," Biometrics, The International Biometric Society, vol. 67(4), pages 1225-1235, December.
  35. Mark A. van de Wiel & Kyung In Kim, 2007. "Estimating the False Discovery Rate Using Nonparametric Deconvolution," Biometrics, The International Biometric Society, vol. 63(3), pages 806-815, September.
  36. Bickel David R., 2012. "Empirical Bayes Interval Estimates that are Conditionally Equal to Unadjusted Confidence Intervals or to Default Prior Credibility Intervals," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(3), pages 1-34, February.
  37. Peter B. Gilbert & Chunyuan Wu & David V. Jobes, 2008. "Genome Scanning Tests for Comparing Amino Acid Sequences Between Groups," Biometrics, The International Biometric Society, vol. 64(1), pages 198-207, March.
  38. Ali Karimnezhad, 2022. "A simple yet efficient method of local false discovery rate estimation designed for genome-wide association data analysis," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 31(1), pages 159-180, March.
  39. Yu, Chang & Zelterman, Daniel, 2017. "A parametric model to estimate the proportion from true null using a distribution for p-values," Computational Statistics & Data Analysis, Elsevier, vol. 114(C), pages 105-118.
  40. Bradley Efron, 2007. "Doing thousands of hypothesis tests at the same time," Metron - International Journal of Statistics, Dipartimento di Statistica, Probabilità e Statistiche Applicate - University of Rome, vol. 0(1), pages 3-21.
  41. Lee, Donghwan & Lee, Youngjo, 2016. "Extended likelihood approach to multiple testing with directional error control under a hidden Markov random field model," Journal of Multivariate Analysis, Elsevier, vol. 151(C), pages 1-13.
  42. Peter Hall & Yvonne Pittelkow & Malay Ghosh, 2008. "Theoretical measures of relative performance of classifiers for high dimensional data with small sample sizes," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 70(1), pages 159-173, February.
  43. Conboy, Lisa Ann & Macklin, Eric & Kelley, John & Kokkotou, Efi & Lembo, Anthony & Kaptchuk, Ted, 2010. "Which patients improve: Characteristics increasing sensitivity to a supportive patient-practitioner relationship," Social Science & Medicine, Elsevier, vol. 70(3), pages 479-484, February.
  44. Patrick Kline & Christopher Walters, 2019. "Audits as Evidence: Experiments, Ensembles, and Enforcement," Papers 1907.06622, arXiv.org, revised Jul 2019.
  45. Iris Ivy M. Gauran & Junyong Park & Johan Lim & DoHwan Park & John Zylstra & Thomas Peterson & Maricel Kann & John L. Spouge, 2018. "Empirical null estimation using zero†inflated discrete mixture distributions and its application to protein domain data," Biometrics, The International Biometric Society, vol. 74(2), pages 458-471, June.
  46. David Ruppert & Dan Nettleton & J. T. Gene Hwang, 2007. "Exploring the Information in p-Values for the Analysis and Planning of Multiple-Test Experiments," Biometrics, The International Biometric Society, vol. 63(2), pages 483-495, June.
  47. Li, Feng & Seillier-Moiseiwitsch, Françoise & Korostyshevskiy, Valeriy R., 2011. "Region-based statistical analysis of 2D PAGE images," Computational Statistics & Data Analysis, Elsevier, vol. 55(11), pages 3059-3072, November.
  48. Montazeri Zahra & Yanofsky Corey M. & Bickel David R., 2010. "Shrinkage Estimation of Effect Sizes as an Alternative to Hypothesis Testing Followed by Estimation in High-Dimensional Biology: Applications to Differential Gene Expression," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-33, June.
  49. Xinge Jessie Jeng & Zhongyin John Daye & Wenbin Lu & Jung-Ying Tzeng, 2016. "Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level," PLOS Computational Biology, Public Library of Science, vol. 12(6), pages 1-23, June.
  50. Shu-Chun Chen & Hsieh Fushing & Chii-Ruey Hwang, 2013. "Discovering focal regions of slightly-aggregated sparse signals," Computational Statistics, Springer, vol. 28(5), pages 2295-2308, October.
  51. Zhao, Haibing & Fung, Wing Kam, 2016. "A powerful FDR control procedure for multiple hypotheses," Computational Statistics & Data Analysis, Elsevier, vol. 98(C), pages 60-70.
  52. Chen, Yunxiao & Lu, Yan & Moustaki, Irini, 2022. "Detection of two-way outliers in multivariate data and application to cheating detection in educational tests," LSE Research Online Documents on Economics 112499, London School of Economics and Political Science, LSE Library.
  53. Shulei Wang, 2023. "Robust differential abundance test in compositional data," Biometrika, Biometrika Trust, vol. 110(1), pages 169-185.
  54. Segal Mark R. & Xiong Hao & Bengtsson Henrik & Bourgon Richard & Gentleman Robert, 2012. "Querying Genomic Databases: Refining the Connectivity Map," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(2), pages 1-37, January.
  55. Michele Guindani & Wesley O. Johnson, 2018. "More nonparametric Bayesian inference in applications," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 27(2), pages 239-251, June.
  56. T. Tony Cai & Weidong Liu, 2016. "Large-Scale Multiple Testing of Correlations," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 111(513), pages 229-240, March.
  57. Yunxiao Chen & Yi-Hsuan Lee & Xiaoou Li, 2022. "Item Pool Quality Control in Educational Testing: Change Point Model, Compound Risk, and Sequential Detection," Journal of Educational and Behavioral Statistics, , vol. 47(3), pages 322-352, June.
  58. T. Tony Cai & Wenguang Sun & Weinan Wang, 2019. "Covariate‐assisted ranking and screening for large‐scale two‐sample inference," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 81(2), pages 187-234, April.
  59. Chen, Shuo & Kang, Jian & Xing, Yishi & Zhao, Yunpeng & Milton, Donald K., 2018. "Estimating large covariance matrix with network topology for high-dimensional biomedical data," Computational Statistics & Data Analysis, Elsevier, vol. 127(C), pages 82-95.
  60. Hong, Zhaoping & Lian, Heng, 2012. "BOPA: A Bayesian hierarchical model for outlier expression detection," Computational Statistics & Data Analysis, Elsevier, vol. 56(12), pages 4146-4156.
  61. Marot Guillemette & Mayer Claus-Dieter, 2009. "Sequential Analysis for Microarray Data Based on Sensitivity and Meta-Analysis," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-33, January.
  62. Sander Greenland, 2005. "Discussion on "Statistical Issues Arising in the Women's Health Initiative"," Biometrics, The International Biometric Society, vol. 61(4), pages 920-921, December.
  63. T. Tony Cai & Wenguang Sun, 2017. "Optimal screening and discovery of sparse signals with applications to multistage high throughput studies," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 79(1), pages 197-223, January.
  64. Chen, Yunxiao & Lee, Yi-Hsuan & Li, Xiaoou, 2022. "Item pool quality control in educational testing: change point model, compound risk, and sequential detection," LSE Research Online Documents on Economics 112498, London School of Economics and Political Science, LSE Library.
  65. Leek Jeffrey T & Storey John D., 2011. "The Joint Null Criterion for Multiple Hypothesis Tests," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-22, June.
  66. Pedro Duarte Silva, A., 2011. "Two-group classification with high-dimensional correlated data: A factor model approach," Computational Statistics & Data Analysis, Elsevier, vol. 55(11), pages 2975-2990, November.
  67. Valencia García, Dalia Jazmin & Lillo Rodríguez, Rosa Elvira & Romo, Juan, 2013. "A Kendall correlation coefficient for functional dependence," DES - Working Papers. Statistics and Econometrics. WS ws133228, Universidad Carlos III de Madrid. Departamento de Estadística.
  68. C. M. Kendziorski & M. Chen & M. Yuan & H. Lan & A. D. Attie, 2006. "Statistical Methods for Expression Quantitative Trait Loci (eQTL) Mapping," Biometrics, The International Biometric Society, vol. 62(1), pages 19-27, March.
  69. Raphael Gottardo & Wei Li & W. Evan Johnson & X. Shirley Liu, 2008. "A Flexible and Powerful Bayesian Hierarchical Model for ChIP–Chip Experiments," Biometrics, The International Biometric Society, vol. 64(2), pages 468-478, June.
  70. Han, Bing & Dalal, Siddhartha R., 2012. "A Bernstein-type estimator for decreasing density with application to p-value adjustments," Computational Statistics & Data Analysis, Elsevier, vol. 56(2), pages 427-437.
  71. Min, Jeong Eun & Whiteside, Matthew D. & Brinkman, Fiona S.L. & McNeney, Brad & Graham, Jinko, 2011. "A statistical approach to high-throughput screening of predicted orthologs," Computational Statistics & Data Analysis, Elsevier, vol. 55(1), pages 935-943, January.
  72. Raphael Gottardo & Adrian E. Raftery & Ka Yee Yeung & Roger E. Bumgarner, 2006. "Bayesian Robust Inference for Differential Gene Expression in Microarrays with Multiple Samples," Biometrics, The International Biometric Society, vol. 62(1), pages 10-18, March.
  73. Sairam Rayaprolu & Zhiyi Chi, 2021. "False Discovery Variance Reduction in Large Scale Simultaneous Hypothesis Tests," Methodology and Computing in Applied Probability, Springer, vol. 23(3), pages 711-733, September.
  74. Xiang, Qinfang & Edwards, Jode & Gadbury, Gary L., 2006. "Interval estimation in a finite mixture model: Modeling P-values in multiple testing applications," Computational Statistics & Data Analysis, Elsevier, vol. 51(2), pages 570-586, November.
  75. Joshua Habiger & Edsel Peña, 2011. "Randomised -values and nonparametric procedures in multiple testing," Journal of Nonparametric Statistics, Taylor & Francis Journals, vol. 23(3), pages 583-604.
  76. Robin, Stephane & Bar-Hen, Avner & Daudin, Jean-Jacques & Pierre, Laurent, 2007. "A semi-parametric approach for mixture models: Application to local false discovery rate estimation," Computational Statistics & Data Analysis, Elsevier, vol. 51(12), pages 5483-5493, August.
  77. Won, Joong-Ho & Lim, Johan & Yu, Donghyeon & Kim, Byung Soo & Kim, Kyunga, 2014. "Monotone false discovery rate," Statistics & Probability Letters, Elsevier, vol. 87(C), pages 86-93.
  78. Wenguang Sun & T. Tony Cai, 2009. "Large‐scale multiple testing under dependence," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 71(2), pages 393-424, April.
  79. Bickel David R., 2008. "Correcting the Estimated Level of Differential Expression for Gene Selection Bias: Application to a Microarray Study," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-27, March.
  80. Dalia Valencia & Rosa E. Lillo & Juan Romo, 2019. "A Kendall correlation coefficient between functional data," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 13(4), pages 1083-1103, December.
  81. Davide Risso & Liam Purvis & Russell B Fletcher & Diya Das & John Ngai & Sandrine Dudoit & Elizabeth Purdom, 2018. "clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets," PLOS Computational Biology, Public Library of Science, vol. 14(9), pages 1-16, September.
  82. Gordon, Alexander & Chen, Linlin & Glazko, Galina & Yakovlev, Andrei, 2009. "Balancing type one and two errors in multiple testing for differential expression of genes," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1622-1629, March.
  83. Yi-Hui Zhou & Paul Brooks & Xiaoshan Wang, 2018. "A Two-Stage Hidden Markov Model Design for Biomarker Detection, with Application to Microbiome Research," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 10(1), pages 41-58, April.
  84. David R. Bickel, 2014. "Small-scale Inference: Empirical Bayes and Confidence Methods for as Few as a Single Comparison," International Statistical Review, International Statistical Institute, vol. 82(3), pages 457-476, December.
  85. Park, DoHwan & Park, Junyong & Zhong, Xiaosong & Sadelain, Michel, 2011. "Estimation of empirical null using a mixture of normals and its use in local false discovery rate," Computational Statistics & Data Analysis, Elsevier, vol. 55(7), pages 2421-2432, July.
  86. Long Qu & Dan Nettleton & Jack C. M. Dekkers, 2012. "A Hierarchical Semiparametric Model for Incorporating Intergene Information for Analysis of Genomic Data," Biometrics, The International Biometric Society, vol. 68(4), pages 1168-1177, December.
  87. He, Li & Sarkar, Sanat K. & Zhao, Zhigen, 2015. "Capturing the severity of type II errors in high-dimensional multiple testing," Journal of Multivariate Analysis, Elsevier, vol. 142(C), pages 106-116.
  88. He, Yi & Pan, Wei & Lin, Jizhen, 2006. "Cluster analysis using multivariate normal mixture models to detect differential gene expression with microarray data," Computational Statistics & Data Analysis, Elsevier, vol. 51(2), pages 641-658, November.
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