Methodological study of affine transformations of gene expression data with proposed robust non-parametric multi-dimensional normalization method

BMC Bioinformatics
Henrik Bengtsson, Ola Hössjer

Abstract

Low-level processing and normalization of microarray data are most important steps in microarray analysis, which have profound impact on downstream analysis. Multiple methods have been suggested to date, but it is not clear which is the best. It is therefore important to further study the different normalization methods in detail and the nature of microarray data in general. A methodological study of affine models for gene expression data is carried out. Focus is on two-channel comparative studies, but the findings generalize also to single- and multi-channel data. The discussion applies to spotted as well as in-situ synthesized microarray data. Existing normalization methods such as curve-fit ("lowess") normalization, parallel and perpendicular translation normalization, and quantile normalization, but also dye-swap normalization are revisited in the light of the affine model and their strengths and weaknesses are investigated in this context. As a direct result from this study, we propose a robust non-parametric multi-dimensional affine normalization method, which can be applied to any number of microarrays with any number of channels either individually or all at once. A high-quality cDNA microarray data set with spike-in co...Continue Reading

References

Jan 23, 1999·Nature Genetics·D J DugganJ M Trent
Apr 25, 2000·Nucleic Acids Research·J SchuchhardtH Herzel
May 8, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M A NewtonK W Tsui
May 18, 2001·Genetical Research·M K Kerr, G A Churchill
May 31, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·M K KerrG A Churchill
Dec 12, 2001·Genome Biology·L RamdasW Zhang
Dec 19, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·D M Rocke, B Durbin
Mar 16, 2002·Microcirculation : the Official Journal of the Microcirculatory Society, Inc·Xinmin LiDavid J Baylink
Mar 26, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Charles KooperbergToshio Tsukiyama
May 10, 2002·Nucleic Acids Research·Tony YuenStuart C Sealfon
Jun 21, 2002·Bioinformatics·Philippe Marc, Claude Jacq
Aug 10, 2002·Bioinformatics·B P DurbinD M Rocke
Apr 5, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Magnus Astrand
May 23, 2003·Bioinformatics·David M Rocke, Blythe Durbin
Jun 14, 2003·Genome Research·Andrea BarczakDavid J Erle
Oct 22, 2004·Journal of Pharmaceutical and Biomedical Analysis·Andrew BlanchardKimberly D Snyder
Nov 16, 2004·BMC Bioinformatics·Henrik BengtssonJohan Vallon-Christersson
Jul 20, 2005·BMC Bioinformatics·Leming ShiJames C Fuscoe
Mar 1, 2006·BMC Bioinformatics·Anders Bengtsson, Henrik Bengtsson
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Xiangqin CuiGary A Churchill

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Citations

Jan 22, 2008·Bioinformatics·H BengtssonT P Speed
Mar 28, 2012·Clinical Journal of Sport Medicine : Official Journal of the Canadian Academy of Sport Medicine·Greg K AlcockPaul W Stratford
Nov 16, 2004·BMC Bioinformatics·Henrik BengtssonJohan Vallon-Christersson
Mar 1, 2006·BMC Bioinformatics·Anders Bengtsson, Henrik Bengtsson
Jul 2, 2011·BMC Genomics·Beth HollowayBailin Li
Dec 7, 2007·PLoS Neglected Tropical Diseases·Joshua FinkMartin L Hibberd
Mar 25, 2009·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Katia ScotlandiPiero Picci
Nov 6, 2007·Electrophoresis·Sandor SpisakAndras Guttman
Apr 23, 2016·BMC Bioinformatics·Xuan ZhuSanjay Shete

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Methods Mentioned

BETA
dissection
PCA

Software Mentioned

aroma
BASE
R
MathType
Axon GenePix Pro

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