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HOME > JOURNALS BY SUBJECT > COMPUTER SCIENCE/MEDICAL AND LIFE SCIENCES > JBCB
Journal of Bioinformatics and Computational Biology (JBCB)
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Volume: 3, Issue: 2(2005) pp. 225-241     DOI: 10.1142/S0219720005001028
Abstract | Full Text (PDF, 639KB) | References
Title: SYSTEMATIC VARIATION NORMALIZATION IN MICROARRAY DATA TO GET GENE EXPRESSION COMPARISON UNBIASED
Copyright of the article belongs to U.S. Government (and the exact ministry/dept of the contributors). Permission has been granted to World Scientific to publish the article as part of this collective work.
Author(s):
JEFF W. CHOU
National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA

RICHARD S. PAULES
National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA

PIERRE R. BUSHEL
Corresponding author.

National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, 27709, USA

North Carolina State University, Raleigh, NC 27695, USA
History:
Received 9 April 2004
Revised 4 June 2004
Accepted 21 June 2004
Abstract:
Normalization removes or minimizes the biases of systematic variation that exists in experimental data sets. This study presents a systematic variation normalization (SVN) procedure for removing systematic variation in two channel microarray gene expression data. Based on an analysis of how systematic variation contributes to variability in microarray data sets, our normalization procedure includes background subtraction determined from the distribution of pixel intensity values from each data acquisition channel and log conversion, linear or non-linear regression, restoration or transformation, and multiarray normalization. In the case when a non-linear regression is required, an empirical polynomial approximation approach is used. Either the high terminated points or their averaged values in the distributions of the pixel intensity values observed in control channels may be used for rescaling multiarray datasets. These pre-processing steps remove systematic variation in the data attributable to variability in microarray slides, assay-batches, the array process, or experimenters. Biologically meaningful comparisons of gene expression patterns between control and test channels or among multiple arrays are therefore unbiased using normalized but not unnormalized datasets.
Keywords:
Microarray; systematic variation; normalization; gene expression; statistics

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