Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases

Background: Quality-control is an important issue in the analysis of gene expression microarrays. One type of problem is regional bias, in which one region of a chip shows artifactually high or low intensities (or ratios in a two-channel array) relative to the majority of the chip. Current practice in quality assessment for microarrays does not address regional biases. Results: We present methods implemented in R for visualizing regional biases and other spatial artifacts on spotted microarrays and Affymetrix chips. We also propose a statistical index to quantify regional bias and investigate its typical distribution on spotted and Affymetrix arrays. We demonstrate that notable regional biases occur on both Affymetrix and spotted arrays and that they can make a significant difference in the case of spotted microarray results. Although strong biases are also seen at the level of individual probes on Affymetrix chips, the gene expression measures are less affected, especially when the R...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Mark Reimers, John N. Weinstein
• Keywords: BMCBI 2005, Chips, Gene Expression, Regional Biases