Stepwise Normalization of Two-Channel Spotted Microarrays

Xiao Yuanyuan, Segal Mark R and Yang Yee Hwa
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Xiao Yuanyuan: University of California, San Francisco
Segal Mark R: University of California, San Francisco
Yang Yee Hwa: University of California, San Francisco

Statistical Applications in Genetics and Molecular Biology, 2005, vol. 4, issue 1, 31

Abstract: Intensities measurements of spotted microarrays embody many undesirable systematic variations. Very commonly, varying amounts and types of such variations are observed in different arrays. Although various normalization methods have been proposed to remove such systematic effects, it has not been well studied how to assess or select the most appropriate method for different arrays and data sets. To address this issue, we present a novel normalization technique, STEPNORM, for data-dependent and adaptive normalization of two-channel spotted microarrays. STEPNORM performs a stepwise interrogation of a range of different normalization models and selects the appropriate method based on formal model selection criteria. In addition, we evaluate the effectiveness of STEPNORM and other commonly used normalization methods utilizing a set of specially constructed splicing arrays.

Keywords: microarrays; normalization; model selection; BIC (search for similar items in EconPapers)
Date: 2005
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DOI: 10.2202/1544-6115.1117

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