A Comparison of Parametric and Nonparametric Methods for Normalising cDNA Microarray Data

Khondoker, Mizanur R., Glasbey, Chris A. and Worton, Bruce J. (2007) A Comparison of Parametric and Nonparametric Methods for Normalising cDNA Microarray Data. Biometrical Journal, 49 (6). pp. 815-823. ISSN 0323-3847

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Abstract

Normalisation is an essential first step in the analysis of most cDNA microarray data, to correct for effects arising from imperfections in the technology. Loess smoothing is commonly used to correct for trends in log-ratio data. However, parametric models, such as the additive plus multiplicative variance model, have been preferred for scale normalisation, though the variance structure of microarray data may be of a more complex nature than can be accommodated by a parametric model. We propose a new nonparametric approach that incorporates location and scale normalisation simultaneously using a Generalised Additive Model for Location, Scale and Shape (GAMLSS, Rigby and Stasinopoulos, 2005, Applied Statistics, 54, 507–554). We compare its performance in inferring differential expression with Huber et al.'s (2002, Bioinformatics, 18, 96–104) arsinh variance stabilising transformation (AVST) using real and simulated data. We show GAMLSS to be as powerful as AVST when the parametric model is correct, and more powerful when the model is wrong. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Item Type: Article
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
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Depositing User: Pure Connector
Date Deposited: 24 Sep 2016 00:41
Last Modified: 24 Jul 2019 22:44
URI: https://ueaeprints.uea.ac.uk/id/eprint/60182
DOI: 10.1002/bimj.200610338

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