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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

Author Affiliations

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

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Genome Biology 2007, 8:R2  doi:10.1186/gb-2007-8-1-r2

Published: 4 January 2007

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.