Bioinformatics Advance Access originally published online on April 1, 2004
Bioinformatics 2004 20(14):2270-2278; doi:10.1093/bioinformatics/bth237
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Bioinformatics 20(14) © Oxford University Press 2004; all rights reserved.
Spot shape modelling and data transformations for microarrays
1 Department of Mathematics and Physics and 2 Plant Biochemistry Laboratory, Department of Plant Biology, Center of Molecular Plant Physiology (PlaCe), Royal Veterinary and Agricultural University, Thorvaldsensvej 40, DK-1871 Frederiksberg C., Denmark
Received on October 30, 2003; revised on March 4, 2004; accepted on March 25, 2004
Advance Access Publication April 1, 2004
Motivation: To study lowly expressed genes in microarray experiments, it is useful to increase the photometric gain in the scanning. However, a large gain may cause some pixels for highly expressed genes to become saturated. Spatial statistical models that model spot shapes on the pixel level may be used to infer information about the saturated pixel intensities. Other possible applications for spot shape models include data quality control and accurate determination of spot centres and spot diameters.
Results: Spatial statistical models for spotted microarrays are studied including pixel level transformations and spot shape models. The models are applied to a dataset from 50mer oligonucleotide microarrays with 452 selected Arabidopsis genes. Logarithmic, Box–Cox and inverse hyperbolic sine transformations are compared in combination with four spot shape models: a cylindric plateau shape, an isotropic Gaussian distribution and a difference of two-scaled Gaussian distribution suggested in the literature, as well as a proposed new polynomial-hyperbolic spot shape model. A substantial improvement is obtained for the dataset studied by the polynomial-hyperbolic spot shape model in combination with the Box–Cox transformation. The spatial statistical models are used to correct spot measurements with saturation by extrapolating the censored data.
Availability: Source code for R is available at http://www.matfys.kvl.dk/~ekstrom/spotshapes/
Contact: ekstrom{at}dina.kvl.dk
* To whom correspondence should be addressed.
Present address: Poalis A/S, Bülowsvej 25, 1870 Frederiksberg C, Denmark
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