Normalization for cDNA microarray data

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, e.g. for differences in labeling efficiency between the two fluorescent dyes. In this case, a constant adjustment is commonly used to force the distribution of the log-ratios to have a median of zero for each slide. However, such global normalization approaches are not adequate in situations where dye biases can depend on spot overall intensity and location on the array (print-tip effects). This paper describes normalization methods that account for intensity and spatial dependence in the ..