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Bioinformatics Vol. 19 no. 7 2003
Pages 825-833
© 2003 Oxford University Press

Non-linear normalization and background correction in one-channel cDNA microarray studies

David Edwards

Department of Biostatistics, Novo Nordisk, Bagsvaerd Denmark

Received on September 9, 2002 ; revised on November 14, 2002 ; accepted on November 15, 2002

Motivation: Data from one-channel cDNA microarray studies may exhibit poor reproducibility due to spatial heterogeneity, non-linear array-to-array variation and problems in correcting for background. Uncorrected, these phenomena can give rise to misleading conclusions.

Results: Spatial heterogeneity may be corrected using two-dimensional loess smoothing (Colantuoni et al., 2002). Non-linear between-array variation may be corrected using an iterative application of one-dimensional loess smoothing. A method for background correction using a smoothing function rather than simple subtraction is described. These techniques promote within-array spatial uniformity and between-array reproducibility. Their application is illustrated using data from a study of the effects of an insulin sensitizer, rosiglitazone, on gene expression in white adipose tissue in diabetic db/db mice. They may also be useful with data from two-channel cDNA microarrays and from oligonucleotide arrays.

Availability: R functions for the methods described are available on request from the author.

Contact: DEd{at}novonordisk.com


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