Signal intensities between samples on a microarrary typically vary by as much as three to four orders of magnitude, frustrating efforts at comparative analysis of samples assayed in parallel. At any given laser power or photomultiplier tube gain (PMTG), some signals will be below detection threshold, while others will have saturated the signal-collection capacity of the scanning device. MicroArray Spot LINEar Regression ("MASLINER") is a software tool that addresses this critical deficiency in scanning technology. MASLINER extends standard linear regression analysis through an innovative formula that recursively computes an aggregated error of regression for data gathered in sequential scans: scans are taken at increasing laser powers or PMTGs, and each linear regression is used to correct for saturation in subsequent, higher powered scans. This enables meaningful comparison of widely varying experimental results in massively-parallel data sets. MASLINER subject to copyright protection and is available for field-exclusive or non-exclusive license.