Microarray image analysis: background estimation using quantile and morphological filters

Background: In a microarray experiment the difference in expression between genes on the same slide is up to 103 fold or more. At low expression, even a small error in the estimate will have great influence on the final test and reference ratios. In addition to the true spot intensity the scanned signal consists of different kinds of noise referred to as background. In order to assess the true spot intensity background must be subtracted. The standard approach to estimate background intensities is to assume they are equal to the intensity levels between spots. In the literature, morphological opening is suggested to be one of the best methods for estimating background this way. Results: This paper examines fundamental properties of rank and quantile filters, which include morphological filters at the extremes, with focus on their ability to estimate between-spot intensity levels. The bias and variance of these filter estimates are driven by the number of background pixels used and the...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Anders Bengtsson, Henrik Bengtsson
• Keywords: BMCBI 2006, Morphological Opening, Rank Filters, True Spot