Abstract

There are many sources of systematic variation in microarray experiments which affect the measured gene expression levels. Normalization is the term used to describe the process of removing such variation. Two-color cDNA microarray experiments are comparative in nature; therefore, commonly used normalization methods focus on adjusting the value of log-intensity ratios between the red and the green channels. This paper reviews some normalization procedures required to ensure that observed differences across spots both within and between slides are reliably measured. In addition, the paper investigates the possibility of obtaining meaningful single-channel information from two-color microarray experiments after careful single-channel normalization.

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