Estimation of expression indexes for oligonucleotide arrays using the singular value decomposition

• 成果类型: Article
• 署名作者: Hu, JH; Wright, FA; Zou, F
• 署名单位: University of Texas System; UTMD Anderson Cancer Center; University of North Carolina; University of North Carolina Chapel Hill
• 刊物名称: JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
• ISSN/ISSBN: 0162-1459
• DOI: 10.1198/016214505000000989
• 发表日期: 2006
• 页码: 41-50
• 关键词: gene-expression; normalization; summaries

摘要

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.