Estimation of expression indexes for oligonucleotide arrays using the singular value decomposition
Estimation of expression indexes for oligonucleotide arrays using the singular value decomposition
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DOI：
10.1198/016214505000000989
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发表时间：
2006-03-01
影响因子：
3.7
通讯作者：
Zou, F
中科院分区：
文献类型：
--
作者：
Hu, JH;Wright, FA;Zou, F
多种寡核苷酸阵列是一种广泛使用的表达微阵列类型，具有吸引人的特征，大量探针用于表示每个转录物。 “表达指数”是一种统计量，用于表示从探针杂交强度估算的特定基因的表达水平。我们表明，Li和Wong提出的一个流行的基于模型的表达索引具有解释是探针强度矩阵的奇异值分解（SVD）的组成部分。遵循此观察，我们提出了一个新的SVD模型，该模型解释了探针之间不同方差结构的不同。我们还建议，强度响应对表达的非线性可以通过数据转换在一定程度上纠正，该数据转换以SVD熵度量为指导。这些方法通过模拟和应用程序进行了两个真实数据集的应用。
Multiprobe oligonucleotide arrays are a widely used type of expression microarray with the attractive feature that numerous probes are used to represent each transcript. An "expression index" is a statistic used to represent expression level for a particular gene that is estimated from the probe hybridization intensities. We show that a popular model-based expression index proposed by Li and Wong has an interpretation as a component of the singular value decomposition (SVD) of the probe intensity matrix. Following this observation, we propose a new SVD model that accounts for differing variance structure across probes. We also propose that nonlinearity in intensity response to expression can be corrected to some extent through a data transformation, which is guided by an SVD entropy measure. The methods are demonstrated with simulation and applications to two real datasets.