Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects
Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects
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DOI：
10.1093/nar/29.12.2549
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发表时间：
2001-06-15
影响因子：
14.9
通讯作者：
Wong, WH
中科院分区：
文献类型：
--
作者：
Tseng, GC;Oh, MK;Wong, WH
我们考虑了使用基因芯片数据比较在两种不同条件下生长的细胞的基因表达水平的问题。我们使用一个质量指数，从同一张幻灯片上的重复斑点计算出来，以过滤掉边远的斑点、质量差的基因和有问题的幻灯片。我们还进行了校准实验，以表明荧光标记之间的归一化是必要的，并且归一化是依赖于幻灯片和非线性的。在对比实验中，提出了一种选择非差异表达基因和构建归一化曲线的秩不变法。在归一化之后，校准数据的残差被用来在对比实验分析中提供关于方差分量的先验信息。基于包含多个水平的变异的分层模型，提出了一种在比较实验中评估基因效应的重要性的方法。这一分析是通过两组实验证实的，分别有125个和4129个基因，在葡萄糖和醋酸盐中生长的大肠杆菌中。
We consider the problem of comparing the gene expression levels of cells grown under two different conditions using cDNA microarray data. We use a quality index, computed from duplicate spots on the same slide, to filter out outlying spots, poor quality genes and problematical slides. We also perform calibration experiments to show that normalization between fluorescent labels is needed and that the normalization is slide dependent and non-linear. A rank invariant method is suggested to select non-differentially expressed genes and to construct normalization curves in comparative experiments. After normalization the residuals from the calibration data are used to provide prior information on variance components in the analysis of comparative experiments. Based on a hierarchical model that incorporates several levels of variations, a method for assessing the significance of gene effects in comparative experiments is presented. The analysis is demonstrated via two groups of experiments with 125 and 4129 genes, respectively, in Escherichia coli grown in glucose and acetate.