斑点cDNA微阵列的重复性分析。
Analysis of repeatability in spotted cDNA microarrays.
作者信息
Jenssen Tor-Kristian, Langaas Mette, Kuo Winston P, Smith-Sørensen Birgitte, Myklebost Ola, Hovig Eivind
机构信息
Department of Computer and Information Science, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
出版信息
Nucleic Acids Res. 2002 Jul 15;30(14):3235-44. doi: 10.1093/nar/gkf441.
Abstract
We report a strategy for analysis of data quality in cDNA microarrays based on the repeatability of repeatedly spotted clones. We describe how repeatability can be used to control data quality by developing adaptive filtering criteria for microarray data containing clones spotted in multiple spots. We have applied the method on five publicly available cDNA microarray data sets and one previously unpublished data set from our own laboratory. The results demonstrate the feasibility of the approach as a foundation for data filtering, and indicate a high degree of variation in data quality, both across the data sets and between arrays within data sets.
摘要
我们报告了一种基于重复点样克隆的可重复性来分析cDNA微阵列数据质量的策略。我们描述了如何通过为包含在多个点上点样的克隆的微阵列数据开发自适应过滤标准，利用可重复性来控制数据质量。我们已将该方法应用于五个公开可用的cDNA微阵列数据集以及我们自己实验室的一个先前未发表的数据集。结果证明了该方法作为数据过滤基础的可行性，并表明数据质量在数据集之间以及数据集中的阵列之间存在高度差异。
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2
Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications.乳腺癌的基因表达模式可区分具有临床意义的肿瘤亚类。
Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10869-74. doi: 10.1073/pnas.191367098.
3
Quantitative quality control in microarray image processing and data acquisition.微阵列图像处理与数据采集中的定量质量控制。
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4
Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects.cDNA微阵列分析中的问题：质量过滤、通道归一化、变异模型及基因效应评估。
Nucleic Acids Res. 2001 Jun 15;29(12):2549-57. doi: 10.1093/nar/29.12.2549.
5
Human prostate cancer and benign prostatic hyperplasia: molecular dissection by gene expression profiling.人类前列腺癌和良性前列腺增生：通过基因表达谱进行分子剖析。
Cancer Res. 2001 Jun 15;61(12):4683-8.
6
An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression.用于检测整体mRNA表达变化的cDNA微阵列性能评估。
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8
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