Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework -: Analysis of global gene expression in Escherichia coli K12
Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework -: Analysis of global gene expression in Escherichia coli K12
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DOI：
10.1074/jbc.m010192200
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发表时间：
2001-06-08
影响因子：
4.8
通讯作者：
Baldi, P
中科院分区：
文献类型：
--
作者：
Long, AD;Mangalam, HJ;Baldi, P
我们描述了基于t检验的统计方法，该方法可以方便地用于高密度阵列数据，以检验治疗之间的统计学显著差异。这些t检验采用治疗组内重复样本间观察到的方差或基于从标准差局部估计值获得的先验估计值的治疗组内重复样本间方差的贝叶斯估计值。贝叶斯先验允许从微阵列数据进行统计推断，即使实验仅在标称水平下重复。我们将这些新的统计检验应用于检查IHF+和IHF-大肠杆菌细胞中差异基因表达模式的数据集（Arfin，S，M.，Long，长叶树A. D、Ito，E. T.，托列里湖Riehle，M. M.，Paegle，E.美国，Hatfield，G. W.（2000）J，Biol. Chem，275，29672-29684）。这些分析鉴定了比使用不结合贝叶斯先验的统计检验鉴定的那些候选基因在生物学上更合理的候选基因组。我们还表明，基于方差分析和贝叶斯先验的统计检验识别基因的上调或下调后的实验操作比仅基于t检验或倍数变化的方法更可靠。所有描述的测试都是在一个简单易用的网络界面中实现的，该界面称为Cyber-T，位于加州大学欧文分校的基因组学网站上。
We describe statistical methods based on the t test that can be conveniently used on high density array data to test for statistically significant differences between treatments. These t tests employ either the observed variance among replicates within treatments or a Bayesian estimate of the variance among replicates within treatments based on a prior estimate obtained from a local estimate of the standard deviation. The Bayesian prior allows statistical inference to be made from microarray data even when experiments are only replicated at nominal levels. We apply these new statistical tests to a data set that examined differential gene expression patterns in IHF+ and IHF- Escherichia coli cells (Arfin, S, M., Long, A. D., Ito, E. T., Tolleri, L., Riehle, M. M., Paegle, E. S., and Hatfield, G. W. (2000) J, Biol. Chem, 275, 29672-29684), These analyses identify a more biologically reasonable set of candidate genes than those identified using statistical tests not incorporating a Bayesian prior. We also show that statistical tests based on analysis of variance and a Bayesian prior identify genes that are up or down-regulated following an experimental manipulation more reliably than approaches based only on a t test or fold change. All the described tests are implemented in a simple-to-use web interface called Cyber-T that is located on the University of California at Irvine genomics web site.