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A statistical model for unwarping of 1-D

Glasbey, C.A. and Vali, L. and Gustafsson, J. (2005) A statistical model for unwarping of 1-D. Electrophoresis, 26 (22). pp. 4327-4242. ISSN 0173-0835

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Abstract

A statistical model is proposed which relates density profiles in 1-D electrophoresis gels, such as those produced by pulsed-field gel electrophoresis (PFGE), to databases of profiles of known genotypes. The warp in each gel lane is described by a trend that is linear in its parameters plus a first-order autoregressive process, and density differences are modelled by a mixture of two normal distributions. Maximum likelihood estimates are computed efficiently by a recursive algorithm that alternates between dynamic time warping to align individual lanes and generalised-least-squares regression to ensure that the warp is smooth between lanes. The method, illustrated using PFGE of Escherichia coli O157 strains, automatically unwarps and classifies gel lanes, and facilitates manual identification of new genotypes

Item type: Article
ID code: 10356
Notes: [1] Vali, L., Wisely, K. A., Pearce, M. C., Turner, E. J., Knight, H. I., Smith, A. W., Amyes, S. G. B., Appl. Environ. Microbiol. 2004, 70, 5947–5954. [2] Barrett, T. J., Lior, H., Green, J. H., Khakharia, R., Wells, J. G., Bell, B. P., Greene, K. D., Lewis, J., Griffin, P. M., J. Clin. Microbiol. 1994, 32, 3013–3017. [3] Goutom, R. K., J. Clin. Microbiol. 1997, 35, 2977–2980. [4] Skovgaard, I. M., Jensen, K., Sondergaard, I., Electrophoresis 1995, 16, 1385–1389. [5] Glasbey, C. A., Horgan, G. W., Image Analysis for the Biological Sciences, Wiley, Chichester 1995. [6] Glasbey, C. A., Mardia, K. V., J. Appl. Stat. 1998 25, 155– 171. [7] Glasbey, C. A., Mardia, K. V., J. R. Stat. Soc. B 2001, 63, 465–514. [8] Glasbey, C. A., Young, M. J., Appl. Stat. 2002, 51, 209–221. [9] Hastie, T. J., Tibshirani, R. J., Generalized Additive Models, Chapman and Hall, London 1990. [10] Bellman, R., Dynamic Programming, Princeton University Press, Princeton 1957. [11] Sakoe, H., Chiba, S., IEEE T. Acous. Speech. 1978, 26, 43– 49. [12] Burr, D. J., IEEE T. Pattern Anal. 1983, 5, 554–559. [13] MacDonald, I. L., Zucchini, W., Hidden Markov and Other Models for Discrete-Valued Time Series, Chapman and Hall, London 1997. [14] Dowsey, A. W., Dunn, M. J., Yang, G.-Z., Proteomics 2003, 3, 1567–1596.
Keywords: autoregressive process, Pulsed-field gel electrophoresis, mixture distribution, image warping, dynamic programming, Pharmacy and materia medica, Biochemistry, Clinical Biochemistry
Subjects: Medicine > Pharmacy and materia medica
Department: Faculty of Science > Strathclyde Institute of Pharmacy and Biomedical Sciences
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    Depositing user: Strathprints Administrator
    Date Deposited: 24 Jun 2011 15:24
    Last modified: 04 Sep 2014 19:44
    URI: http://strathprints.strath.ac.uk/id/eprint/10356

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