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PubMed · 12724292

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

David Edwards
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Abstract

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.

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Adipose TissueAnimalsArtifactsCarbocyaninesGene Expression ProfilingMaleMiceModels, GeneticModels, StatisticalNonlinear DynamicsOligonucleotide Array Sequence AnalysisQuality ControlRNAReproducibility of ResultsSensitivity and SpecificitySequence Analysis, DNAStochastic ProcessesComparative StudyEvaluation StudyJournal ArticleValidation Study

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David Edwards. 2003-05-01. Non-linear normalization and background correction in one-channel cDNA microarray studies.. https://doi.org/10.1093/bioinformatics%2Fbtg083

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