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Extending the Dynamic Range of Signal Intensities in DNA Microarrays
Choi D1, O’Malley JP2 , Lasarev MR3 , Lapidus J1, Lu X2, Pattee P2, Nagalla 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
ABSTRACT
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