There is no silver bullet: a guide to low-level data transforms and normalisation methods for microarray data

• Published in: Briefings in bioinformatics Vol. 6; no. 1; pp. 86 - 97
• Main Authors: KREIL, David P, RUSSELL, Roslin R
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.03.2005; Oxford Publishing Limited (England)
• Subjects: Algorithms; Bioinformatics; Biological and medical sciences; Calibration - standards; Data analysis; Data Interpretation, Statistical; Design of experiments; Fundamental and applied biological sciences. Psychology; Gene expression; Gene Expression Profiling - instrumentation; Gene Expression Profiling - methods; Gene Expression Profiling - standards; General aspects; Genetic Variation - genetics; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Genetic; Models, Statistical; Numerical Analysis, Computer-Assisted; Oligonucleotide Array Sequence Analysis - instrumentation; Oligonucleotide Array Sequence Analysis - methods; Oligonucleotide Array Sequence Analysis - standards; Sequence Analysis, DNA - instrumentation; Sequence Analysis, DNA - methods; Sequence Analysis, DNA - standards; Data analysis; Experimental data; Bias; Prediction; DNA chip; low-level data- transforms; data normalisation; Review; Microarray; experimental bias; Clusterin; microarrays; Statistical test; Computer program; microarray data analysis; Classification; Robustness; Bioinformatics
• ISSN: 1467-5463; 1477-4054
• DOI: 10.1093/bib/6.1.86

To overcome random experimental variation, even for simple screens, data from multiple microarrays have to be combined. There are, however, systematic differences between arrays, and any bias remaining after experimental measures to ensure consistency needs to be controlled for. It is often difficult to make the right choice of data transformation and normalisation methods to achieve this end. In this tutorial paper we review the problem and a selection of solutions, explaining the basic principles behind normalisation procedures and providing guidance for their application.