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Because transcript abundances vary over many orders of magnitude while abundances of oligos in calibrated references are constant, no single scanner setting can measure all experimental and reference spot intensities within the linear range. To address this issue we developed a procedure in which an array is scanned multiple times at different laser power or PMT settings and a software program masliner (MicroArray Spot LINEar Regression) combines the linear ranges of each scan onto a common linear scale, effectively extending the signal intensity range.
Left: A single array scanned at multiple PMT gains. Dim features are not seen in the low sensitivity scan (above), but when gain is increased brighter features saturate (below). Right: masliner corrects for saturation by using the linear regression of feature intensities in the linear range in both scans ( ) to map saturated values ( ) onto the same linear scale ( ).
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