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

A number of methods have been proposed to incorporate multiple scans at different intensities to reduce the quantification error and to minimize effects of saturation, but no direct comparison of their efficacy has been made. Here we used 40 technical replicates to compare 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 a variety of metrics Keywords: Multiple Scans Agilent 22K oligonucleotide microarrays were used to examine the reproducibility of data from 3 scans at different PMT settings and from data obtained from 3 methods that incorporate data from multiple scans. In this study the Stratagene Universal Mouse RNA reference was used.