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題名 DNA微陣列基因顯著性分析驗證
作者 蘇慧玲
貢獻者 薛慧敏
蘇慧玲
關鍵詞 整體誤差率
多重比較方法
錯誤發現率
日期 2002
上傳時間 2009-09-14
摘要 摘 要
     
     在基因微陣列(DNA microarrays)的技術中,可同時得到數以千筆的資料,為了找出具有顯著差異的基因,一般會考慮控制整體誤差率(familywise error rate,FWE) 的多重比較方法(multiple comparison procedures,MCP)。但當基因數或假設檢定個數過多時,其檢定會產生不易拒絕虛無假設的結果,使得結論過於保守。為解決此一問題,Benjamini & Hochberg(1995)建議採用控制錯誤發現率(false discovery rate,FDR)的方法來替代整體誤差率FWE。且Tusher et al.(2001)在DNA微陣列顯著分析(significance analysis of microarrays,SAM)的文章中提出利用排列分佈(permutations)估計錯誤發現率FDR的方法。本篇論文將介紹Tusher et al.(2001)所提出的SAM估計錯誤發現率FDR的方法,且提出一修正SAM方法:SAMM。另外介紹兩種控制顯著水準的統計方法:SAME和SAMT(t檢定)。透過電腦模擬驗證四種方法其錯誤發現率FDR的表現。
Abstract
     
     
     DNA microarray technology provides tools enable to simultaneously study thousands of genes. A conservative multiple comparison procedure (MCP) controlling the familywise type I error rate (FWE) is considered. However, the conservativeness of a MCP becomes more and more severe as the number of comparisons (genes) increases. Instead of FWE, another error rate, the false discovery rate (FDR), is suggested. Tusher et al.(2001) proposed a statistical procedure, the Significance Analysis of Microarrays (SAM), to analyze a microarray data set. In which, the conclusion is drawn at a specific threshold and the false discovery rate (FDR) of the conclusion is estimated by permutations. In this paper, inspired by the SAM, three other methods are proposed. The performances of these methods are investigated and compared through simulations.
參考文獻 參考文獻
Benjamini, Y. & Hochberg, Y. (1995) “Controlling the false discovery rate: a practical and powerful approach to multiple testing”. J. R. Stat. Soc.Ser. B-Methodological, 57,289-300.
Efron, B. & Tibshirani, R. J. (1993) “An Introduction to the Bootstrap.” Chapman & Hall.
Kerr, M. K., Afshari, C. A., Bennett, L., Bushel, P., Martinez, J., Walker, N. J. and Churchill, G. A. (2001) “Statistical Analysis of a Gene Expression Microarray Experiment with Replication”. Statistica Sinica, 12, 203-218.
Kerr, M.K., Martin, M., and Churchill G.A. (2000). “Analysis of Variance for Gene Expres-sion Microarray Data.” Journal of Computational Biology, 7, 819-837.
Kikuchi, H., Hossain, A., Yoshida, H., and Kobayashi, S. (1998). “Induction of Cytochrome P-450 1A1 by Omeprazole in Human HepG2 Cells is Protein Tyrosine Kinase-Dependent and is Not Inhibited by Alpha-Naphtho avone.” Archives of Biochemical Biophysics , 358, 351-358.
Li, W., Harper, P.A., Tang, B.K., and Okey A.B. (1998). “Regulation of Cytochrome
P450 Enzymes by Aryl Hydrocarbon Receptor in Human Cells: CYP1A2 Expression
in the LS180 Colon Carcinoma Cell Line after Treatment with ,3,7,8-
Tetrachlorodibenzo-p-dioxin or 3-Methylcholanthrene.” Biochemical Pharmacology,
56, 599-612.
Nadon, R. & Shoemaker, J. (2002) “Statistical issues with microarrays: processing and analysis”. Trends in Genetics, 18, 265-271.
Soric, B. (1989) “ Statistical “discoveries” and effect size estimation.” J. Am. Statist. Ass., 84, 608-610.
Simes, R. J. (1986) “An improved Bonferroni procedure for multiple tests of significance”. Biometrika, 73, 751-754.
Storey, J. D. & Tibshirani, R. (2003) “SAM thresholding and false discovery rates for detecting differential gene expression”. In The Analysis of Gene Expression Data: Methods and Software, by G Parmigiani, ES Garrett, RA Irizarry and SL Zeger (editors). Springer, New York. Available at http://www.stat.berkeley.edu/~storey/.
Tusher, V. G., Tibshirani, R., and Chu, G.(2001) “ Significance analysis of microarrays applied to the ionizing radiation response” Proc. Natl. Acad. Sci. USA, 98,5116-5121.
Yang, Y.H., Dudoit, S., Luu, P., and Speed, T.P. (2000) “Normalization for cDNA Microar-ray Data”. Technical report 589, Department of Statistics, University of California, Berkeley. Available at http://www.stat.berkeley.edu/users/terry/zarray
/Html/papersindex.html/.
描述 碩士
國立政治大學
統計研究所
90354005
91
資料來源 http://thesis.lib.nccu.edu.tw/record/#G0090354005
資料類型 thesis
dc.contributor.advisor 薛慧敏zh_TW
dc.contributor.author (Authors) 蘇慧玲zh_TW
dc.creator (作者) 蘇慧玲zh_TW
dc.date (日期) 2002en_US
dc.date.accessioned 2009-09-14-
dc.date.available 2009-09-14-
dc.date.issued (上傳時間) 2009-09-14-
dc.identifier (Other Identifiers) G0090354005en_US
dc.identifier.uri (URI) https://nccur.lib.nccu.edu.tw/handle/140.119/30873-
dc.description (描述) 碩士zh_TW
dc.description (描述) 國立政治大學zh_TW
dc.description (描述) 統計研究所zh_TW
dc.description (描述) 90354005zh_TW
dc.description (描述) 91zh_TW
dc.description.abstract (摘要) 摘 要
     
     在基因微陣列(DNA microarrays)的技術中,可同時得到數以千筆的資料,為了找出具有顯著差異的基因,一般會考慮控制整體誤差率(familywise error rate,FWE) 的多重比較方法(multiple comparison procedures,MCP)。但當基因數或假設檢定個數過多時,其檢定會產生不易拒絕虛無假設的結果,使得結論過於保守。為解決此一問題,Benjamini & Hochberg(1995)建議採用控制錯誤發現率(false discovery rate,FDR)的方法來替代整體誤差率FWE。且Tusher et al.(2001)在DNA微陣列顯著分析(significance analysis of microarrays,SAM)的文章中提出利用排列分佈(permutations)估計錯誤發現率FDR的方法。本篇論文將介紹Tusher et al.(2001)所提出的SAM估計錯誤發現率FDR的方法,且提出一修正SAM方法:SAMM。另外介紹兩種控制顯著水準的統計方法:SAME和SAMT(t檢定)。透過電腦模擬驗證四種方法其錯誤發現率FDR的表現。
zh_TW
dc.description.abstract (摘要) Abstract
     
     
     DNA microarray technology provides tools enable to simultaneously study thousands of genes. A conservative multiple comparison procedure (MCP) controlling the familywise type I error rate (FWE) is considered. However, the conservativeness of a MCP becomes more and more severe as the number of comparisons (genes) increases. Instead of FWE, another error rate, the false discovery rate (FDR), is suggested. Tusher et al.(2001) proposed a statistical procedure, the Significance Analysis of Microarrays (SAM), to analyze a microarray data set. In which, the conclusion is drawn at a specific threshold and the false discovery rate (FDR) of the conclusion is estimated by permutations. In this paper, inspired by the SAM, three other methods are proposed. The performances of these methods are investigated and compared through simulations.
en_US
dc.description.tableofcontents 目 錄
     
     第一章 緒論 .....................................1
     第二章 SAM .....................................4
     第一節 固定門檻值(Δ)之統計方法..................4
     1.1 SAM .....................................4
     1.2 SAMM ....................................7
     第二節 固定顯著水準(α)之統計方法................8
     2.1 SAME .....................................8
     2.2 t檢定(SAMT)...............................8
      第三節 錯誤發現率FDR之估計.......................8
     第三章 模擬.....................................9
     第一節 固定門檻值................................11
     第二節 固定顯著水準..............................16
     第四章 實例....................................21
     第五章 結論………………………………………………24
     
     參考文獻 ……………………………………………………25
     附錄:實例程式
zh_TW
dc.language.iso en_US-
dc.source.uri (資料來源) http://thesis.lib.nccu.edu.tw/record/#G0090354005en_US
dc.subject (關鍵詞) 整體誤差率zh_TW
dc.subject (關鍵詞) 多重比較方法zh_TW
dc.subject (關鍵詞) 錯誤發現率zh_TW
dc.title (題名) DNA微陣列基因顯著性分析驗證zh_TW
dc.type (資料類型) thesisen
dc.relation.reference (參考文獻) 參考文獻zh_TW
dc.relation.reference (參考文獻) Benjamini, Y. & Hochberg, Y. (1995) “Controlling the false discovery rate: a practical and powerful approach to multiple testing”. J. R. Stat. Soc.Ser. B-Methodological, 57,289-300.zh_TW
dc.relation.reference (參考文獻) Efron, B. & Tibshirani, R. J. (1993) “An Introduction to the Bootstrap.” Chapman & Hall.zh_TW
dc.relation.reference (參考文獻) Kerr, M. K., Afshari, C. A., Bennett, L., Bushel, P., Martinez, J., Walker, N. J. and Churchill, G. A. (2001) “Statistical Analysis of a Gene Expression Microarray Experiment with Replication”. Statistica Sinica, 12, 203-218.zh_TW
dc.relation.reference (參考文獻) Kerr, M.K., Martin, M., and Churchill G.A. (2000). “Analysis of Variance for Gene Expres-sion Microarray Data.” Journal of Computational Biology, 7, 819-837.zh_TW
dc.relation.reference (參考文獻) Kikuchi, H., Hossain, A., Yoshida, H., and Kobayashi, S. (1998). “Induction of Cytochrome P-450 1A1 by Omeprazole in Human HepG2 Cells is Protein Tyrosine Kinase-Dependent and is Not Inhibited by Alpha-Naphtho avone.” Archives of Biochemical Biophysics , 358, 351-358.zh_TW
dc.relation.reference (參考文獻) Li, W., Harper, P.A., Tang, B.K., and Okey A.B. (1998). “Regulation of Cytochromezh_TW
dc.relation.reference (參考文獻) P450 Enzymes by Aryl Hydrocarbon Receptor in Human Cells: CYP1A2 Expressionzh_TW
dc.relation.reference (參考文獻) in the LS180 Colon Carcinoma Cell Line after Treatment with ,3,7,8-zh_TW
dc.relation.reference (參考文獻) Tetrachlorodibenzo-p-dioxin or 3-Methylcholanthrene.” Biochemical Pharmacology,zh_TW
dc.relation.reference (參考文獻) 56, 599-612.zh_TW
dc.relation.reference (參考文獻) Nadon, R. & Shoemaker, J. (2002) “Statistical issues with microarrays: processing and analysis”. Trends in Genetics, 18, 265-271.zh_TW
dc.relation.reference (參考文獻) Soric, B. (1989) “ Statistical “discoveries” and effect size estimation.” J. Am. Statist. Ass., 84, 608-610.zh_TW
dc.relation.reference (參考文獻) Simes, R. J. (1986) “An improved Bonferroni procedure for multiple tests of significance”. Biometrika, 73, 751-754.zh_TW
dc.relation.reference (參考文獻) Storey, J. D. & Tibshirani, R. (2003) “SAM thresholding and false discovery rates for detecting differential gene expression”. In The Analysis of Gene Expression Data: Methods and Software, by G Parmigiani, ES Garrett, RA Irizarry and SL Zeger (editors). Springer, New York. Available at http://www.stat.berkeley.edu/~storey/.zh_TW
dc.relation.reference (參考文獻) Tusher, V. G., Tibshirani, R., and Chu, G.(2001) “ Significance analysis of microarrays applied to the ionizing radiation response” Proc. Natl. Acad. Sci. USA, 98,5116-5121.zh_TW
dc.relation.reference (參考文獻) Yang, Y.H., Dudoit, S., Luu, P., and Speed, T.P. (2000) “Normalization for cDNA Microar-ray Data”. Technical report 589, Department of Statistics, University of California, Berkeley. Available at http://www.stat.berkeley.edu/users/terry/zarrayzh_TW
dc.relation.reference (參考文獻) /Html/papersindex.html/.zh_TW