【論】Dudoit,2002,Statistical methods for identifyin～

Sandrine Dudoit, Yee Hwa Yang, Matthew J.Callow and Terence P.Speed.
Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments.
Statistica Sinica 12(2002), 111-139
[PDF][Web Site]

・マイクロアレイデータの統計解析の概観とその応用。
・データ：マウス。正常(control)×8、apo AI gene knocked-out×8、合計16サンプル。257遺伝子。
・遺伝子抽出法：adjusted p-values

・「Given suitably normalized data, the biological question of differential expression is restated as a problem in multiple hypothesis testing: the simultaneous test for each gene of the null hypothesis of no association between the expression levels and the treatment/control status.」
・手順「Our basic approach for identifying differentially expressed genes consists of two steps: (1) computing a test statistic for each gene, and (2) obtaining adjusted p-values for a multiple testing procedure which strongly controls the family-wise Type I error rate and takes into account the dependence structure between the gene expression levels.」
・「To date, attention has focused primarily on expression at the transcription stage, i.e., on mRNA or transcript levels.」
・目的「The goal of the study is to identify genes with altered expression in the livers of two lines of mice with very low HDL cholesterol levels compared to inbred control mice.」
・注意点「Note that the spotted cDNA sequences are usually referred to as "genes", whether they are actual genes, ESTs (expressed sequence tags), or DNA sequences from other sources.」

・内容がつかめない。図（M-A plot）の見方がわからず。

《チェック論文》
・Chen, Y., Dougherty, E. R. and Bittner, M. L. (1997). Ratio-based decisions and the quantitative analysis of cDNA microarray images. J. Biomedical Optics 2, 364-374.
・Kerr, M. K. and Churchill, G. A. (2001). Experimental design for gene expression microarrays. Biostatistics 2, 183-201.