A new approach to intensity-dependent normalization of two-channel microarrays
A new approach to intensity-dependent normalization of two-channel microarrays
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DOI：
10.1093/biostatistics/kxj038
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发表时间：
2007-01-01
期刊：
影响因子：
2.1
通讯作者：
Storey, John D.
中科院分区：
文献类型：
--
作者：
Dabney, Alan R.;Storey, John D.
双通道微阵列测量来自一对生物样品的数千个基因的相对表达水平。为了可靠地比较阵列之间和阵列内的基因表达水平，有必要去除使感兴趣的生物信号失真的系统误差。实现这一点的标准是平滑"MA图"，以消除强度依赖性染料偏差和阵列特异性效应。然而，MA方法需要强假设，这限制了它们的普遍适用性。我们回顾这些假设，并得出几个实际的情况下，他们失败了。"染料交换"归一化方法的使用频率要低得多，因为它每对样本需要两个阵列。我们表明，染料交换是准确的一般假设下，即使在强度依赖的染料偏置，染料交换去除染料偏置一般从一对样本。基于mRNA量和单通道荧光强度之间的关系的灵活模型，我们证明了染料交换方法的普遍适用性。然后，我们提出了一个共同的阵列染料交换（CADS）的方法规范化的双通道微阵列。我们表明，CADS消除了染料偏见和阵列特异性的影响，并保留了真实的差异表达信号的模型的假设下，每个基因。
A two-channel microarray measures the relative expression levels of thousands of genes from a pair of biological samples. In order to reliably compare gene expression levels between and within arrays, it is necessary to remove systematic errors that distort the biological signal of interest. The standard for accomplishing this is smoothing "MA-plots" to remove intensity-dependent dye bias and array-specific effects. However, MA methods require strong assumptions, which limit their general applicability. We review these assumptions and derive several practical scenarios in which they fail. The "dye-swap" normalization method has been much less frequently used because it requires two arrays per pair of samples. We show that a dye-swap is accurate under general assumptions, even under intensity-dependent dye bias, and that a dye-swap removes dye bias from a single pair of samples in general. Based on a flexible model of the relationship between mRNA amount and single-channel fluorescence intensity, we demonstrate the general applicability of a dye-swap approach. We then propose a common array dye-swap (CADS) method for the normalization of two-channel microarrays. We show that CADS removes both dye bias and array-specific effects, and preserves the true differential expression signal for every gene under the assumptions of the model.