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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 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
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