Local Mean Normalization of Microarray Element Signal Intensities across an Array Surface: Quality Control and Correction of Spatially Systematic Artifacts. (June 2002)

• Record Type: Journal Article
• Authors: Colantuoni, Carlo; Henry, George; Zeger, Scott; Pevsne, Jonathan
• Is Part Of: Biotechniques. Volume 32:Number 6(2002)
• Page Start: 1316
• Page End: 1320
• Publication Date: 2002-06
• Subjects: Biology, Experimental -- Periodicals; Molecular biology -- Periodicals; Medical technology -- Periodicals; Biology, Experimental; Medical technology; Molecular biology; Clinical Laboratory Techniques -- Periodicals; Research -- Periodicals; Medical Laboratory Science -- Periodicals; Periodicals; Electronic journals; 570
• DOI: 10.2144/02326mt02
• Languages: English
• ISSNs: 0736-6205

Abstract

Here we present a methodology for the normalization of element signal intensities to a mean intensity calculated locally across the surface of a DNA microarray. These methods allow the detection and/or correction of spatially systematic artifacts in microarray data. These include artifacts that can be introduced during the robotic printing, hybridization, washing, or imaging of microarrays. Using array element signal intensities alone, this local mean normalization process can correct for such artifacts because they vary across the surface of the array. The local mean normalization can be used for quality control and data correction purposes in the analysis of microarray data. These algorithms assume that array elements are not spatially ordered with regard to sequence or biological function and require that this spatial mapping is identical between the two sets of intensities to be compared. The tool described in this report was developed in the R statistical language and is freely available on the Internet as part of a larger gene expression analysis package. This Web implementation is interactive and user-friendly and allows the easy use of the local mean normalization tool described here, without programming expertise or downloading of additional software.