Quality assessment of affymetrix GeneChip data
Quality assessment of affymetrix GeneChip data
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DOI：
10.1089/omi.2006.10.358
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发表时间：
2006-09-01
影响因子：
3.3
通讯作者：
Sick, Beate
中科院分区：
文献类型：
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作者：
Heber, Steffen;Sick, Beate
Affymetrix GeneChips 是最成熟的微阵列平台之一。这种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且耗时的工作，存在许多潜在的不需要的变异来源，如果不加控制，可能会损害结果。不断增加的数据量和数据复杂性引发了人们对评估生成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，我们概述了用于 Affymetrix GeneChip 数据质量评估的当前方法和软件工具。我们专注于质量指标、诊断图、探针级方法、伪图像和分类方法来识别损坏的芯片。我们还描述了 RNA 质量评估方法，这些方法在挑战 RNA 来源（如福尔马林包埋活检、激光显微解剖样本或单细胞）方面发挥着重要作用。本文未讨论湿实验室方法。
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.