Controlling mixed directional false discovery rate in multidimensional decisions with applications to microarray studies
Controlling mixed directional false discovery rate in multidimensional decisions with applications to microarray studies
复制标题
控制多维决策中的混合方向错误发现率及其在微阵列研究中的应用
DOI：
10.1007/s11749-017-0547-1
复制
发表时间：
2018-06-01
期刊：
影响因子：
1.3
通讯作者：
Fung，Wing Kam
中科院分区：
文献类型：
--
作者：
Zhao，Haibing;Fung，Wing Kam
时间进程微阵列实验在几个时间点采集样本。为了揭示基因表达随时间的动态变化，我们需要识别有意义的基因，并检测可能带来方向性错误的基因表达模式。郭等人(Biometrics 66(2)：485-492,2010)引入了混合定向错误发现率(MdFDR)控制程序，该程序控制所有拒绝中类型I和类型III错误的预期比例之和。本文发展了mdFDR控制的加权p值程序，给出了保证(渐近)mdFDR控制的一些充分条件。给出了满足充分条件的一些权值及其估计量。通过大量仿真，将所提出的加权dpValue方法与现有方法进行了比较。基于提出的加权取值过程，我们提供了控制错误覆盖率(FCR)的多个CI。我们使用所提出的方法来分析Lobenhofer等人(Mol Endocrinol 16：1215-1229,2002)中研究的时间进程微阵列数据。我们的大多数发现与现有方法得到的结果是相同的。此外，我们还发现了其他一些重要的基因，如CDKN3和NQO1。
Time-course microarray experiments harvested samples at several time points. To reveal the dynamic gene expression changes over time, we need to identify the significant genes and detect the patterns of gene expressions, which may bring directional errors. Guo et al. (Biometrics 66(2):485–492, 2010) introduced a mixed directional false discovery rate (mdFDR) controlled procedure, which controls the sum of expected proportions of Type I and Type III errors among all rejections. In this paper, we develop weightedpvalue procedures for mdFDR control and give out some sufficient conditions to assure the (asymptotic) mdFDR control. Some weights and their estimators are illustrated to satisfy the sufficient conditions. The proposed weightedpvalue procedures are compared with the existing method by extensive simulations. Based on the proposed weightedpvalues procedure, we provide multiple CIs which control the false coverage-statement rate (FCR). We use the proposed methods to analyze the time-course microarray data studied in Lobenhofer et al. (Mol Endocrinol 16:1215–1229, 2002). Most of our findings are the same as those obtained by the existing method. In addition, we identify some other important genes, such as CDKN3 and NQO1.