title: The use of background signal in the transformation of cDNA-microarray measurements.
abstract: As the application field of microarrays grows, so does the need for appropriate statistical tools to analyse the signal intensity measurements. Normalisation procedures are required to make the signals from different channels and arrays comparable. One objective, which is also the focus of this report, is to remove the curvature seen on plots of the log ratio versus the mean log intensity values of two channels.A number of methods already exist that are based on the assumption of a shift between the measurements of the two channels. In this article, we explore the use of background measurements to estimate and correct for the shift. We compare our proposal with some well known methods by applying them to microarrays from two studies. These two studies investigate the effect of vegetable diets on the gene expression in colon and lung tissue of mice. Graphical illustrations and a robust summary statistic show that all transformations are an improvement to the raw data. Overall, the best results are obtained with our proposed transformation that takes the background measurements into account.
authors.affiliation: Center for Statistics, Hasselt University, Agoralaan, Diepenbeek, Belgium. suzy.vansanden@uhasselt.be
authors.forename: Suzy
authors.initials: S
authors.lastname: Van Sanden
authors.forename: Tomasz
authors.initials: T
authors.lastname: Burzykowski
mesh_terms: D000465:Algorithms; D001530:Belgium; D002138:Calibration; D017404:In Situ Hybridization, Fluorescence / Q000379:methods* / Q000592:standards; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D010783:Photometry / Q000379:methods; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013050:Spectrometry, Fluorescence / Q000379:methods*