Effects of scanning sensitivity and multiple scan algorithms on microarray data quality

Background: Maximizing the utility of DNA microarray data requires optimization of data acquisition through selection of an appropriate scanner setting. To increase the amount of useable data, several approaches have been proposed that incorporate multiple scans at different sensitivities to reduce the quantification error and to minimize effects of saturation. However, no direct comparison of their efficacy has been made. In the present study we compared individual scans at low, medium and high sensitivity with three methods for combining data from multiple scans (either 2-scan or 3-scan cases) using an actual dataset comprising 40 technical replicates of a reference RNA standard. Results: Of the individual scans, the low scan exhibited the lowest background signal, the highest signal-to-noise ratio, and equivalent reproducibility to the medium and high scans. Most multiple scan approaches increased the range of probe intensities compared to the individual scans, but did not increase...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Andrew Williams, Errol M. Thomson
• Keywords: BMCBI 2010, Individual Scans, Multiple Scan, Scan