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Activity Number:
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23
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Type:
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Contributed
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Date/Time:
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Sunday, August 6, 2006 : 2:00 PM to 3:50 PM
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Sponsor:
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Biometrics Section
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| Abstract - #305411 |
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Title:
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Two Extensions of the TW-SLM for Systematically Incorporating Control Genes and Spot Quality Information To Improve Normalization of cDNA Microarray Data
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Author(s):
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Deli Wang*+ and Cun-Hui Zhang and Marcelo B. Soares and Jian Huang
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Companies:
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The University of Alabama at Birmingham and Rutgers University and Northwestern University and The University of Iowa
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Address:
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1824 6th Ave., S., Birmingham, AL, 35294,
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Keywords:
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microarray ; spike ; normalization ; quality control ; semi-parametric model
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Abstract:
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Normalization and data quality control are basic steps in microarray data analysis. Proper normalization and data quality control ensure the intensity ratios provide meaningful and accurate measurement of relative gene expression values. Side information, including control genes (e.g., spike-in genes), and spot quality information is available in a typical microarray dataset, but it is not utilized fully by many normalization and quality-control methods. We propose two extensions of the two-way semi-linear model (TW-SLM) for appropriately combining control genes and spot quality information to improve normalization of cDNA microarray data. A new quality score also is derived and can be used independently for spot quality assessment. We used two datasets produced by specially designed microarray experiments to demonstrate the proposed methods.
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