Quality Assessment of Affymetrix GeneChip Data
Quality Assessment of Affymetrix GeneChip Data
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DOI：
10.1007/0-387-29362-0_3
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发表时间：
2005
期刊：
影响因子：
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通讯作者：
B. Bolstad;F. Collin;J. Brettschneider;K. Simpson;L. Cope;R. Irizarry;T. Speed
中科院分区：
文献类型：
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作者：
B. Bolstad;F. Collin;J. Brettschneider;K. Simpson;L. Cope;R. Irizarry;T. Speed
Affymetrix GeneChips是最成熟的微阵列平台之一。这项强大的技术允许用户同时测量数千个基因的表达。然而，微阵列实验是一项复杂而耗时的工作，有许多不想要的变异的潜在来源，如果不加以控制，可能会影响结果。不断增加的数据量和数据复杂性引发了人们对评估所产生的微阵列数据质量的重要性的日益关注和认识。在这篇综述中，我们对Affymetrix基因芯片数据质量评估的现有方法和软件工具进行概述。我们专注于质量指标、诊断图、探测级方法、伪图像和分类方法来识别损坏的芯片。我们还描述了在挑战诸如福尔马林包埋活组织检查、激光显微解剖样本或单细胞等RNA来源时发挥重要作用的RNA质量评估方法。本文不讨论湿法实验室方法。
Affymetrix GeneChips are one of the best established microarray platforms. This powerful technique allows users to measure the expression of thousands of genes simultaneously. However, a microarray experiment is a sophisticated and time consuming endeavor with many potential sources of unwanted variation that could compromise the results if left uncontrolled. Increasing data volume and data complexity have triggered growing concern and awareness of the importance of assessing the quality of generated microarray data. In this review, we give an overview of current methods and software tools for quality assessment of Affymetrix GeneChip data. We focus on quality metrics, diagnostic plots, probe-level methods, pseudo-images, and classification methods to identify corrupted chips. We also describe RNA quality assessment methods which play an important role in challenging RNA sources like formalin embedded biopsies, laser-micro dissected samples, or single cells. No wet-lab methods are discussed in this paper.