Non-linear normalization and background correction in one-channel cDNA microarray studies
Non-linear normalization and background correction in one-channel cDNA microarray studies
复制标题
DOI：
10.1093/bioinformatics/btg083
复制
发表时间：
2003-05-01
期刊：
影响因子：
5.8
通讯作者：
Edwards, D
中科院分区：
文献类型：
--
作者：
Edwards, D
动机：由于空间异质性、阵列间非线性变异和背景校正问题，单通道cDNA微阵列研究的数据可能表现出较差的再现性。如果不加以纠正，这些现象可能会产生误导性的结论。结果：空间异质性可以使用二维黄土平滑进行纠正（Colantuoni等人，2002年）。阵列间的非线性变化可以使用一维黄土平滑的迭代应用来校正。描述了一种使用平滑函数而不是简单减法的背景校正方法。这些技术促进了阵列内空间均匀性和阵列间再现性。他们的应用说明使用的数据从一个研究的影响，胰岛素增敏剂，罗格列酮，在糖尿病db/db小鼠的白色脂肪组织的基因表达。他们也可能是有用的数据从双通道cDNA微阵列和寡核苷酸阵列。
Motivation: Data from one-channel cDNA microarray studies may exhibit poor reproducibility due to spatial heterogeneity, non-linear array-to-array variation and problems in correcting for background. Uncorrected, these phenomena can give rise to misleading conclusions.Results: Spatial heterogeneity may be corrected using two-dimensional loess smoothing (Colantuoni et al., 2002). Non-linear between-array variation may be corrected using an iterative application of one-dimensional loess smoothing. A method for background correction using a smoothing function rather than simple subtraction is described. These techniques promote within-array spatial uniformity and between-array reproducibility. Their application is illustrated using data from a study of the effects of an insulin sensitizer, rosiglitazone, on gene expression in white adipose tissue in diabetic db/db mice. They may also be useful with data from two-channel cDNA microarrays and from oligonucleotide arrays.