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 the dynamic range (the proportion of useable data). Approaches displayed striking differences in the background signal and signal-to-noise ratio. However, increased probe intensity range and improved signal-to-noise ratios did not necessarily correlate with improved reproducibility. Importantly, for one multiple scan method that combined 3 scans, reproducibility was significantly improved relative to individual scans and all other multiple scan approaches. The same method using 2 scans yielded significantly lower reproducibility, attributable to a lack-of-fit of the statistical model. Conclusions Our data indicate that implementation of a suitable multiple scan approach can improve reproducibility, but that model validation is critical to ensure accurate estimates of probe intensity.
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