Liu Fang, Kuo Winston P, Jenssen Tor-Kristian, Hovig Eivind
Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, Oslo, Norway.
Methods Mol Biol. 2012;802:141-55. doi: 10.1007/978-1-61779-400-1_10.
With genome-wide gene expression microarrays being increasingly applied in various areas of biomedical research, the diversity of platforms and analytical methods has made comparison of data from multiple platforms very challenging. In this chapter, we describe a generalized framework for systematic comparisons across gene expression profiling platforms, which could accommodate both the available commercial arrays and "in-house" platforms, with both one-dye and two-dye platforms. It includes experimental design, data preprocessing protocols, cross-platform gene matching approaches, measures of data consistency comparisons, and considerations in biological validation. In the design of this framework, we considered the variety of platforms available, the need for uniform quality control procedures, real-world practical limitations, statistical validity, and the need for flexibility and extensibility of the framework. Using this framework, we studied ten diverse microarray platforms, and we conclude that using probe sequences matched at the exon level is important to improve cross-platform data consistency compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values, as confirmed by QRT-PCR. After stringent preprocessing, commercial arrays were more consistent than "in-house" arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.
随着全基因组基因表达微阵列在生物医学研究的各个领域中越来越广泛地应用，平台和分析方法的多样性使得来自多个平台的数据比较极具挑战性。在本章中，我们描述了一个用于跨基因表达谱平台进行系统比较的通用框架，该框架可以兼容现有的商业阵列和“自制”平台，包括单染料和双染料平台。它包括实验设计、数据预处理方案、跨平台基因匹配方法、数据一致性比较的度量以及生物验证中的注意事项。在设计这个框架时，我们考虑了可用平台的多样性、统一质量控制程序的必要性、实际应用中的限制、统计有效性以及框架的灵活性和可扩展性。使用这个框架，我们研究了十个不同的微阵列平台，并且得出结论：与基于注释的匹配相比，使用在外显子水平匹配的探针序列对于提高跨平台数据一致性很重要。一般来说，如通过定量逆转录聚合酶链反应（QRT-PCR）所证实的，高表达基因的一致性良好，而低表达值基因的一致性则有所不同。经过严格的预处理后，商业阵列比“自制”阵列更具一致性，并且在大多数度量标准下，单染料平台比双染料平台更具一致性。
