Improved statistical tests for differential gene expression by shrinking variance components estimates
Improved statistical tests for differential gene expression by shrinking variance components estimates
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DOI：
10.1093/biostatistics/kxh018
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发表时间：
2005-01-01
期刊：
影响因子：
2.1
通讯作者：
Churchill, GA
中科院分区：
文献类型：
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作者：
Cui, XG;Hwang, JTG;Churchill, GA
在微阵列数据的统计分析中组合跨基因的信息是期望的，因为对于每个单独的基因获得的数据点的数量相对较少。这里.我们开发了一种误差方差的估计器，该估计器可以使用James-Stein收缩概念跨基因借用信息。利用该估计量构造了一个新的检验统计量（F-S）。将新统计量与用于检验差异表达的其他统计量进行比较：基因特异性F检验（F-1）、合并方差F统计量（F-3）、使用个体和合并方差平均值的混合统计量（F-2）、正则化t统计量、后验概率统计量B。和SAM t检验F-S检验显示了在广泛的模拟数据中检测差异表达基因的最佳或新的最佳功效，其中与单个基因相关的方差分量是同质的或异质的。因此，F-S提供了一种强大而稳健的方法来测试基因的差异表达，该方法利用了个体基因测试方法中不可用的信息，并且不会受到合并方差方法的偏倚。
Combining information across genes in the statistical analysis of microarray data is desirable because of the relatively small number of data points obtained for each individual gene. Here. we develop an estimator of the error variance that can borrow information across genes using the James-Stein shrinkage concept. A new test statistic (F-S) is constructed using this estimator. The new statistic is compared with other statistics used to test for differential expression: the gene-specific F test (F-1), the pooled-variance F statistic (F-3), a hybrid statistic (F-2) that uses the average of the individual and pooled variances, the regularized t-statistic, the posterior odds statistic B. and the SAM t-test. The F-S-test shows best or newly best power for detecting differentially expressed genes over a wide range of simulated data in which the variance components associated with individual genes are either homogeneous or heterogeneous. Thus F-S provides a powerful and robust approach to test differential expression of genes that utilizes information not available in individual gene testing approaches and does not suffer from biases of the pooled variance approach.