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

Mizanur R. Khondoker, Chris A. Glasbey, Bruce J. Worton

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)

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)
Original languageEnglish
Pages (from-to)815-823
Number of pages9
JournalBiometrical Journal
Volume49
Issue number6
Early online date26 Apr 2007
DOIs
Publication statusPublished - Dec 2007

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