Analysis of Background Correction Methods for DNA Microarray Imaging

Abstract

Most microarray image scanning approaches provide an estimation of the intensity of the foreground and background for each spot. Background intensity must be corrected in order to remove the effect of the non‐specific binding or spatial heterogeneity across the array, but when such corrections are applied many problems appear, such as negative intensity for the spot or high variability of low‐intensity log ratios. In this paper, many alternative methods for calculating background intensity are discussed and many approaches for background correction are tested and compared. GenePix, ScanAlyze and QuantArry are the methods reviewed for background intensity extraction. Four methods for background correction were examined and the Edwards method was found to be the best and most suitable method.