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Online Journal of Bioinformatics ©

 7 (1) : 46-56, 2006.

Extending the Dynamic Range of Signal Intensities in DNA Microarrays.



Choi D1,  O’Malley JP2 , Lasarev MR3Lapidus J1, Lu X2, Pattee P2Nagalla SR2 


1 Division of Biostatistics, Department of Public Health and Preventive Medicine, 2 Center for Biomarker Discovery, Department of Pediatrics, 3 Center for Research on Occupational and Environmental Toxicology,  Oregon Health & Science University , Oregon, USA




Choi D,  O’Malley JP, Lasarev MR,  Lapidus J, Lu X, Pattee P,  Nagalla SR, Extending the Dynamic Range of Signal Intensities in DNA Microarrays, Online J Bioinformatics, 7 (1) 46-56, 2006. The accuracy of gene expression ratios obtained from DNA microarrays depends upon the fluorescence intensity of the signals being within the dynamic range of scanner. Signals produced for certain spots of microarrays can sometimes be too low (below noise) or too high (saturated) to be accurately read by the scanner. The intensity below noise or above saturation can cause bias that cannot be corrected for conventional normalization methods. To expand the dynamic range of scanner, we developed an algorithm that can merge two separate scans of each fluorescent label on an array. A method was developed in which each label of a dual-channel DNA microarray is scanned twice at two different scanner settings to produce high and low scan intensities. By using a nonlinear regression model, the two separate scans are merged. The merged data consist of the intensities of higher signal-to-noise ratios for non-saturated spots in high scan and the adjusted intensities from the nonlinear regression model for underestimated high intensity spots due to saturation. The saturation point in high scan is estimated as a parameter in the model. Four dual-channel DNA microarrays were employed to test the merging algorithm. The merging procedure recovered saturated intensities that were above signal saturation in either or both channels while screening out outliers. It was concluded that by merging data from two separate laser scans of each fluorescent label on an array, the potential bias in signal intensities due to below noise or above saturation can be avoided providing more accurate estimates of true differential expression as well as an increase in usable spots.

Key words: Microarray, Dynamic range, Merge, Scanner, Multiple scan