Receiver operating characteristic analysis: a general tool for DNA array data filtration and performance estimation
Receiver operating characteristic analysis: a general tool for DNA array data filtration and performance estimation
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DOI：
10.1016/s0888-7543(02)00042-3
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发表时间：
2003-02-01
期刊：
影响因子：
4.4
通讯作者：
Pelizzari, CA
中科院分区：
文献类型：
--
作者：
Khodarev, NN;Park, J;Pelizzari, CA
DNA阵列分析的关键步骤是数据过滤，它可以将数千个检测到的信号减少到有限的基因组。目前还没有普遍接受的过滤规则。我们提出了一个合理的方法，阈值的强度与截止水平的基础上，估计受试者工作特征（ROC）分析。该技术将测试结果与已知的阳性和阴性信号分布进行比较。我们将该方法应用于Atlas cDNA阵列，GeneFilters和Affyssin GeneChip。ROC分析表明，这些不同系统的假阳性和真阳性数据的分布相似。我们说明了基于强度的过滤的最佳截止水平的估计，提供最高的真假信号的比率。对于基因芯片阵列，我们推导出的过滤阈值与基于重复杂交的报告数据一致。使用ROC优化的基于强度的过滤与其他类型的过滤（例如，基于差异和/或比率的显著性）相结合，应该改善DNA阵列分析。ROC方法也证明了不同类型的阵列，成像仪和分析软件的性能比较。(C)2003 Elsevier Science（美国）。All rights reserved.
A critical step for DNA array analysis is data filtration, which can reduce thousands of detected signals to limited sets of genes. Commonly accepted rules for such filtration are still absent. We present a rational approach, based on thresholding of intensities with cutoff levels that are estimated by receiver operating characteristic (ROC) analysis. The technique compares test results with known distributions of positive and negative signals. We apply the method to Atlas cDNA arrays, GeneFilters, and Affymetrix GeneChip. ROC analysis demonstrates similarities in the distribution of false and true positive data for these different systems. We illustrate the estimation of an optimal cutoff level for intensity-based filtration, providing the highest ratio of true to false signals. For GeneChip arrays, we derived filtration thresholds consistent with the reported data based on replicate hybridizations. Intensity-based filtration optimized with ROC combined with other types of filtration (for example, based on significances of differences and/or ratios), should improve DNA array analysis. ROC methodology is also demonstrated for comparison of the performance of different types of arrays, imagers, and analysis software. (C) 2003 Elsevier Science (USA). All rights reserved.