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Proceedings Paper

Normalization for cDNA microarry data
Author(s): Yee Hwa Yang; Sandrine Dudoit; Percy Luu; Terence P. Speed
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Paper Abstract

There are many sources of systematic variation in microarray experiments which affect the measured gene expression levels. Normalization is the term used to describe the process of removing such variation, e.g. for differences in labeling efficiency between the two fluorescent dyes. In this case, a constant adjustment is commonly used to force the distribution of the log-ratios to have a median of zero for each slide. However, such global normalization approaches are not adequate in situations where dy biases can depend on spot overall intensity and location on the array (print-tip effects). This paper describes normalization methods that account for intensity and spatial dependence in the dye biases for different types of cDNA microarray experiments, including dye-swap experiments. In addition, the choice of the subset of genes to use fo normalization is discussed. The subset selected may be different for experiments where only a few genes are expected to be differentially expressed and those where a majority of genes are expected to change. The proposed approaches are illustrated using gene expression data from a study of lipid metabolism in mice.

Paper Details

Date Published: 4 June 2001
PDF: 12 pages
Proc. SPIE 4266, Microarrays: Optical Technologies and Informatics, (4 June 2001); doi: 10.1117/12.427982
Show Author Affiliations
Yee Hwa Yang, Univ. of California/Berkeley (United States)
Sandrine Dudoit, Stanford Univ. (United States)
Percy Luu, Univ. of California/Berkeley (United States)
Terence P. Speed, Univ. of California/Berkeley and The Walter and Eliza Hall Institute (United States)

Published in SPIE Proceedings Vol. 4266:
Microarrays: Optical Technologies and Informatics
Michael L. Bittner; Yidong Chen; Andreas N. Dorsel; Edward R. Dougherty, Editor(s)

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