Method

Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes

Alicia Oshlack , Dianne Emslie , Lynn M Corcoran and Gordon K Smyth

Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, Victoria, Australia

author email corresponding author email

Genome Biology 2007, 8:R2doi:10.1186/gb-2007-8-1-r2

Published:	4 January 2007

Subject areas: Bioinformatics, Genome studies

Abstract

Normalization is critical for removing systematic variation from microarray data. For two-color microarray platforms, intensity-dependent lowess normalization is commonly used to correct relative gene expression values for biases. Here we outline a normalization method for use when the assumptions of lowess normalization fail. Specifically, this can occur when specialized boutique arrays are constructed that contain a subset of genes selected to test particular biological functions.