Multiple Hypothesis Testing in Microarray Experiments

Statistical Science - Tập 18 Số 1 - 2003
Sandrine Dudoit, Juliet Popper Shaffer, Jennifer C. Boldrick

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Tài liệu tham khảo

Westfall, P. H. and Young, S. S. (1993). <i>Resampling-based Multiple Testing: Examples and Methods for $p$-Value Adjustment</i>. Wiley, New York.

Šidák, Z. (1967). Rectangular confidence regions for the means of multivariate normal distributions. <i>J. Amer. Statist. Assoc.</i> <b>62</b> 626--633.

Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. <i>J. Roy. Statist. Soc. Ser. B</i> <b>57</b> 289--300.

Benjamini, Y. and Yekutieli, D. (2001). The control of the false discovery rate in multiple testing under dependency. <i>Ann. Statist.</i> <b>29</b> 1165--1188.

Brown, P. O. and Botstein, D. (1999). Exploring the new world of the genome with DNA microarrays. <i>Nature Genetics</i> <b>21</b> 33--37.

Efron, B., Tibshirani, R., Storey, J. D. and Tusher, V. (2001). Empirical Bayes analysis of a microarray experiment. <i>J. Amer. Statist. Assoc.</i> <b>96</b> 1151--1160.

Simes, R. J. (1986). An improved Bonferroni procedure for multiple tests of significance. <i>Biometrika</i> <b>73</b> 751--754.

Ihaka, R. and Gentleman, R. (1996). R: A language for data analysis and graphics. <i>J. Comput. Graph. Statist.</i> <b>5</b> 299--314.

Hochberg, Y. (1988). A sharper Bonferroni procedure for multiple tests of significance. <i>Biometrika</i> <b>75</b> 800--802.

Holm, S. (1979). A simple sequentially rejective multiple test procedure. <i>Scand. J. Statist.</i> <b>6</b> 65--70.

Lönnstedt, I. and Speed, T. P. (2002). Replicated microarray data. <i>Statist. Sinica</i> <b>12</b> 31--46.

Scheffé, H. (1959). <i>The Analysis of Variance</i>. Wiley, New York.

Hochberg, Y. and Tamhane, A. C. (1987). <i>Multiple Comparison Procedures</i>. Wiley, New York.

Lehmann, E. L. (1986). <i>Testing Statistical Hypotheses</i>, 2nd ed. Wiley, New York.

Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M., Downing, J. R., Caligiuri, M. A., Bloomfield, C. D. and Lander, E. S. (1999). Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. <i>Science</i> <b>286</b> 531--537.

Newton, M. A., Kendziorski, C. M., Richmond, C. S., Blattner, F. R. and Tsui, K. W. (2001). On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data. <i>Journal of Computational Biology</i> <b>8</b> 37--52.

Tusher, V. G., Tibshirani, R. and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. <i>Proc. Natl. Acad. Sci. U.S.A.</i> <b>98</b> 5116--5121.

Yang, Y. H., Dudoit, S., Luu, P. and Speed, T. P. (2001). Normalization for cDNA microarray data. In <i>Microarrays: Optical Technologies and Informatics</i> (M. L. Bittner, Y. Chen, A. N. Dorsel and E. R. Dougherty, eds.) 141--152. SPIE, Bellingham, WA.

Alizadeh, A. A., Eisen, M. B., Davis, R. E., Ma, C., Lossos, I. S., Rosenwald, A., Boldrick, J. C., Sabet, H., Tran, T., Yu, X., Powell, J. I., Yang, L., Marti, G. E., Moore, T., Hudson Jr., J., Lu, L., Lewis, D. B., Tibshirani, R., Sherlock, G., Chan, W. C., Greiner, T. C., Weisenburger, D. D., Armitage, J. O., Warnke, R., Levy, R., Wilson, W., Grever, M. R., Byrd, J. C., Botstein, D., Brown, P. O. and Staudt, L. M. (2000). Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. <i>Nature</i> <b>403</b> 503--511.

Alon, U., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S., Mack, D. and Levine, A. J. (1999). Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. <i>Proc. Natl. Acad. Sci. U.S.A.</i> <b>96</b> 6745--6750.

Beran, R. (1988). Balanced simultaneous confidence sets. <i>J. Amer. Statist. Assoc.</i> <b>83</b> 679--686.

Boldrick, J. C., Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. L., Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O. and Relman, D. A. (2002). Stereotyped and specific gene expression programs in human innate immune responses to bacteria. <i>Proc. Natl. Acad. Sci. U.S.A.</i> <b>99</b> 972--977.

Braver, S. L. (1975). On splitting the tails unequally: A new perspective on one- versus two-tailed tests. <i>Educational and Psychological Measurement</i> <b>35</b> 283--301.

Buckley, M. J. (2000). <i>The Spot User's Guide</i>. CSIRO Mathematical and Information Sciences, North Ryde, NSW, Australia. Available at http://www.cmis.csiro.au/IAP/Spot/ spotmanual.htm.

Callow, M. J., Dudoit, S., Gong, E. L., Speed, T. P. and Rubin, E. M. (2000). Microarray expression profiling identifies genes with altered expression in HDL-deficient mice. <i>Genome Research</i> <b>10</b> 2022--2029.

Chu, G., Goss, V., Narasimhan, B. and Tibshirani, R. (2000). SAM (Significance Analysis of Microarrays)---Users guide and technical document. Technical report, Stanford Univ.

Dudoit, S., Shaffer, J. P. and Boldrick, J. C. (2002). Multiple hypothesis testing in microarray experiments. Technical Report 110, Division of Biostatistics, Univ. California, Berkeley. Available at http://www.bepress.com/ucbbiostat/ paper110/.

Dudoit, S., Yang, Y. H., Callow, M. J. and Speed, T. P. (2002). Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. <i>Statist. Sinica</i> <b>12</b> 111--139.

Dunn, O. J. (1958). Estimation of the means of dependent variables. <i>Ann. Math. Statist.</i> <b>29</b> 1095--1111.

Efron, B., Storey, J. D. and Tibshirani, R. (2001). Microarrays, empirical Bayes methods, and false discovery rates. Technical Report 2001-23B/217, Dept. Statistics, Stanford Univ.

Efron, B., Tibshirani, R., Goss, V. and Chu, G. (2000). Microarrays and their use in a comparative experiment. Technical Report 2000-37B/213, Dept. Statistics, Stanford Univ.

Finner, H. (1999). Stepwise multiple test procedures and control of directional errors. <i>Ann. Statist.</i> <b>27</b> 274--289.

Gabriel, K. R. (1975). A comparison of some methods of simultaneous inference in MANOVA. In <i>Multivariate Statistical Methods: Among-Groups Covariation</i> (W. R. Atchley and E. H. Bryant, eds.) 61--80. Dowden, Hutchinson and Ross, Stroudsburg, PA.

Ge, Y., Dudoit, S. and Speed, T. P. (2003). Resampling-based multiple testing for microarray data analysis. <i>TEST</i>. To appear.

Genovese, C. and Wasserman, L. (2001). Operating characteristics and extensions of the FDR procedure. Technical Report 737, Dept. Statistics, Carnegie Mellon Univ.

Hommel, G. (1988). A stagewise rejective multiple test procedure based on a modified Bonferroni test. <i>Biometrika</i> <b>75</b> 383--386.

Hommel, G. and Bernhard, G. (1999). Bonferroni procedures for logically related hypotheses. <i>J. Statist. Plann. Inference</i> <b>82</b> 119--128.

Jogdeo, K. (1977). Association and probability inequalities. <i>Ann. Statist.</i> <b>5</b> 495--504.

Kerr, M. K., Martin, M. and Churchill, G. A. (2000). Analysis of variance for gene expression microarray data. <i>Journal of Computational Biology</i> <b>7</b> 819--837.

Krishnaiah, P. R. and Reising, J. M. (1985). Multivariate multiple comparisons. <i>Encyclopedia of Statistical Sciences</i> <b>6</b> 88--95. Wiley, New York.

Lipshutz, R. J., Fodor, S., Gingeras, T. R. and Lockhart, D. J. (1999). High density synthetic oligonucleotide arrays. <i>Nature Genetics</i> <b>21</b> 20--24.

Manduchi, E., Grant, G. R., McKenzie, S. E., Overton, G. C., Surrey, S. and Stoeckert Jr., C. J. (2000). Generation of patterns from gene expression data by assigning confidence to differentially expressed genes. <i>Bioinformatics</i> <b>16</b> 685--698.

Mayo, D. and Spanos, A. (2002). A severe testing interpretation of Neyman--Pearson tests. Unpublished.

Morrison, D. F. (1990). <i>Multivariate Statistical Methods</i>, 3rd ed. McGraw-Hill, New York.

National Reading Panel (1999). Teaching children to read. Report, National Institute of Child Health and Human Development, National Institutes of Health.

Pepe, M. S., Longton, G., Anderson, G. L. and Schummer, M. (2003). Selecting differentially expressed genes from microarray experiments. <i>Biometrics</i> <b>59</b>. To appear.

Perou, C. M., Jeffrey, S. S., van de Rijn, M., Rees, C. A., Eisen, M. B., Ross, D. T., Pergamenschikov, A., Williams, C. F., Zhu, S. X., Lee, J. C. F., Lashkari, D., Shalon, D., Brown, P. O. and Botstein, D. (1999). Distinctive gene expression patterns in human mammary epithelial cells and breast cancers. <i>Proc. Natl. Acad. Sci.</i> <b>96</b> 9212--9217.

Pollack, J. R., Perou, C. M., Alizadeh, A. A., Eisen, M. B., Pergamenschikov, A., Williams, C. F., Jeffrey, S. S., Botstein, D. and Brown, P. O. (1999). Genome-wide analysis of DNA copy-number changes using cDNA microarrays. <i>Nature Genetics</i> <b>23</b> 41--46.

Pollard, K. S. and van der Laan, M. J. (2003). Resampling-based multiple testing with asymptotic strong control of type I error. Submitted.

Ramsey, P. H. (1978). Power differences between pairwise multiple comparisons. <i>J. Amer. Statist. Assoc.</i> <b>73</b> 479--485.

Reiner, A., Yekutieli, D. and Benjamini, Y. (2001). Using resampling-based FDR controlling multiple test procedures for analyzing microarray gene expression data. Unpublished.

Rom, D. M. (1990). A sequentially rejective test procedure based on a modified Bonferroni inequality. <i>Biometrika</i> <b>77</b> 663--665.

Ross, D. T., Scherf, U., Eisen, M. B., Perou, C. M., Rees, C., Spellman, P., Iyer, V., Jeffrey, S. S., van de Rijn, M., Waltham, M., Pergamenschikov, A., Lee, J. C. F., Lashkari, D., Shalon, D., Myers, T. G., Weinstein, J. N., Botstein, D. and Brown, P. O. (2000). Systematic variation in gene expression patterns in human cancer cell lines. <i>Nature Genetics</i> <b>24</b> 227--234.

Seeger, P. (1968). A note on a method for the analysis of significances en masse. <i>Technometrics</i> <b>10</b> 586--593.

Shaffer, J. P. (1986). Modified sequentially rejective multiple test procedures. <i>J. Amer. Statist. Assoc.</i> <b>81</b> 826--831.

Shaffer, J. P. (1995). Multiple hypothesis testing: A review. <i>Annual Review of Psychology</i> <b>46</b> 561--584.

Shaffer, J. P. (2002). Multiplicity, directional (Type III) errors, and the null hypothesis. <i>Psychological Methods</i> <b>7</b> 356--369.

Sorić, B. (1989). Statistical ``discoveries'' and effect-size estimation. <i>J. Amer. Statist. Assoc.</i> <b>84</b> 608--610.

Storey, J. D. (2001). The false discovery rate: A Bayesian interpretation and the q-value. Technical Report 2001-12, Dept. Statistics, Stanford Univ.

Storey, J. D. (2002). A direct approach to false discovery rates. <i>J. R. Stat. Soc. Ser. B Stat. Methodol.</i> <b>64</b> 479--498.

Storey, J. D. and Tibshirani, R. (2001). Estimating the positive false discovery rate under dependence, with applications to DNA microarrays. Technical Report 2001-28, Dept. Statistics, Stanford Univ.

Tibshirani, R., Hastie, T., Narasimhan, B., Eisen, M., Sherlock, G., Brown, P. and Botstein, D. (2002). Exploratory screening of genes and clusters from microarray experiments. <i>Statist. Sinica</i> <b>12</b> 47--59.

Troendle, J. F. (1996). A permutational step-up method of testing multiple outcomes. <i>Biometrics</i> <b>52</b> 846--859.

van der Laan, M. J. and Bryan, J. (2001). Gene expression analysis with the parametric bootstrap. <i>Biostatistics</i> <b>2</b> 445--461.

Westfall, P. H., Zaykin, D. V. and Young, S. S. (2001). Multiple tests for genetic effects in association studies. In <i>Biostatistical Methods</i> (S. Looney, ed.) 143--168. Humana, Totowa, NJ.

Wright, S. P. (1992). Adjusted $p$-values for simultaneous inference. <i>Biometrics</i> <b>48</b> 1005--1013.

Yang, Y. H., Buckley, M. J., Dudoit, S. and Speed, T. P. (2002). Comparison of methods for image analysis on cDNA microarray data. <i>J. Comput. Graph. Statist.</i> <b>11</b> 108--136.

Yekutieli, D. and Benjamini, Y. (1999). Resampling-based false discovery rate controlling multiple test procedures for correlated test statistics. <i>J. Statist. Plann. Inference</i> <b>82</b> 171--196.