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Resampling-based multiple testing for microarray data analysis

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  • Youngchao Ge
  • Sandrine Dudoit
  • Terence Speed

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  • Youngchao Ge & Sandrine Dudoit & Terence Speed, 2003. "Resampling-based multiple testing for microarray data analysis," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 12(1), pages 1-77, June.
    • Handle: RePEc:spr:testjl:v:12:y:2003:i:1:p:1-77
    DOI: 10.1007/BF02595811
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    References listed on IDEAS

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    1. Efron B. & Tibshirani R. & Storey J.D. & Tusher V., 2001. "Empirical Bayes Analysis of a Microarray Experiment," Journal of the American Statistical Association, American Statistical Association, vol. 96, pages 1151-1160, December.
    2. John D. Storey, 2002. "A direct approach to false discovery rates," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 64(3), pages 479-498, August.
    3. Westfall P. H. & Soper K. A., 2001. "Using Priors to Improve Multiple Animal Carcinogenicity Tests," Journal of the American Statistical Association, American Statistical Association, vol. 96, pages 827-834, September.
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    1. Edward L. Korn & Boris Freidlin, 2008. "A Note on Controlling the Number of False Positives," Biometrics, The International Biometric Society, vol. 64(1), pages 227-231, March.
    2. Tsai, Chen-An & Chen, James J., 2007. "Kernel estimation for adjusted p-values in multiple testing," Computational Statistics & Data Analysis, Elsevier, vol. 51(8), pages 3885-3897, May.
    3. Ebrahimi, Nader, 2008. "Simultaneous control of false positives and false negatives in multiple hypotheses testing," Journal of Multivariate Analysis, Elsevier, vol. 99(3), pages 437-450, March.
    4. Guo Wenge & Peddada Shyamal, 2008. "Adaptive Choice of the Number of Bootstrap Samples in Large Scale Multiple Testing," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 7(1), pages 1-21, March.
    5. Dazard, Jean-Eudes & Sunil Rao, J., 2012. "Joint adaptive mean–variance regularization and variance stabilization of high dimensional data," Computational Statistics & Data Analysis, Elsevier, vol. 56(7), pages 2317-2333.
    6. Debashis Ghosh, 2006. "Shrunken p-Values for Assessing Differential Expression with Applications to Genomic Data Analysis," Biometrics, The International Biometric Society, vol. 62(4), pages 1099-1106, December.
    7. Yifan Gu & Yang Qi & Pulin Gong, 2019. "Rich-club connectivity, diverse population coupling, and dynamical activity patterns emerging from local cortical circuits," PLOS Computational Biology, Public Library of Science, vol. 15(4), pages 1-34, April.
    8. Jesse Hemerik & Jelle Goeman, 2018. "Exact testing with random permutations," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 27(4), pages 811-825, December.
    9. Wu, Jincao & Patwa, Tasneem H. & Lubman, David M. & Ghosh, Debashis, 2009. "Identification of differentially expressed spatial clusters using humoral response microarray data," Computational Statistics & Data Analysis, Elsevier, vol. 53(8), pages 3094-3102, June.
    10. Ge, Yongchao & Sealfon, Stuart C. & Tseng, Chi-Hong & Speed, Terence P., 2007. "A Holm-type procedure controlling the false discovery rate," Statistics & Probability Letters, Elsevier, vol. 77(18), pages 1756-1762, December.
    11. Miecznikowski, Jeffrey C. & Gold, David & Shepherd, Lori & Liu, Song, 2011. "Deriving and comparing the distribution for the number of false positives in single step methods to control k-FWER," Statistics & Probability Letters, Elsevier, vol. 81(11), pages 1695-1705, November.
    12. Baolin Wu & Zhong Guan & Hongyu Zhao, 2006. "Parametric and Nonparametric FDR Estimation Revisited," Biometrics, The International Biometric Society, vol. 62(3), pages 735-744, September.
    13. Kai Yu & William Wheeler & Qizhai Li & Andrew W. Bergen & Neil Caporaso & Nilanjan Chatterjee & Jinbo Chen, 2010. "A Partially Linear Tree-based Regression Model for Multivariate Outcomes," Biometrics, The International Biometric Society, vol. 66(1), pages 89-96, March.
    14. Zhenchuan Wang & Qiuying Sha & Shuanglin Zhang, 2016. "Joint Analysis of Multiple Traits Using "Optimal" Maximum Heritability Test," PLOS ONE, Public Library of Science, vol. 11(3), pages 1-12, March.
    15. Lippmann, Quentin, 2022. "Gender and lawmaking in times of quotas," Journal of Public Economics, Elsevier, vol. 207(C).
    16. Pittelkow Yvonne E & Wilson Susan R, 2003. "Visualisation of Gene Expression Data - the GE-biplot, the Chip-plot and the Gene-plot," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 2(1), pages 1-19, September.
    17. Sheng, Xuguang & Yang, Jingyun, 2013. "An adaptive truncated product method for combining dependent p-values," Economics Letters, Elsevier, vol. 119(2), pages 180-182.
    18. Xuesong Yu & Timothy W. Randolph & Hua Tang & Li Hsu, 2010. "Detecting Genomic Aberrations Using Products in a Multiscale Analysis," Biometrics, The International Biometric Society, vol. 66(3), pages 684-693, September.
    19. Bergamelli, Michele & Bianchi, Annamaria & Khalaf, Lynda & Urga, Giovanni, 2019. "Combining p-values to test for multiple structural breaks in cointegrated regressions," Journal of Econometrics, Elsevier, vol. 211(2), pages 461-482.
    20. Richard Luger, 2024. "Regularizing stock return covariance matrices via multiple testing of correlations," Papers 2407.09696, arXiv.org.
    21. 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.
    22. Mark van der Laan & Sandrine Dudoit & Katherine Pollard, 2004. "Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate," U.C. Berkeley Division of Biostatistics Working Paper Series 1138, Berkeley Electronic Press.
    23. Fu, Hsuan & Luger, Richard, 2022. "Multiple testing of the forward rate unbiasedness hypothesis across currencies," Journal of Empirical Finance, Elsevier, vol. 68(C), pages 232-245.

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