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A Nonlinear Mixed-Effects Model for Estimating Calibration Intervals for Unknown Concentrations in Two-Color Microarray Data with Spike-Ins

Author

Listed:
  • Thilakarathne Pushpike J

    (Catholic University of Leuven and University of Hasselt)

  • Verbeke Geert

    (Catholic University of Leuven and University of Hasselt)

  • Engelen Kristof

    (Catholic University of Leuven)

  • Marchal Kathleen

    (Catholic University of Leuven)

Abstract

In this study, we propose a calibration method for preprocessing spiked-in microarray experiments based on nonlinear mixed-effects models. This method uses a spike-in calibration curve to estimate normalized absolute expression values. Moreover, using the asymptotic properties of the calibration estimate, 100(1-?)% confidence intervals for the estimated expression values can be constructed. Simulations are used to show that the approximations on which the construction of the confidence intervals are based are sufficiently accurate to reach the desired coverage probabilities. We illustrate applicability of our method, by estimating the normalized absolute expression values together with the corresponding confidence intervals for two publicly available cDNA microarray experiments (Hilson et al., 2004; Smets et al., 2008). This method can easily be adapted to preprocess one-color oligonucleotide microarray data with a slight adjustment to the mixed model.

Suggested Citation

  • Thilakarathne Pushpike J & Verbeke Geert & Engelen Kristof & Marchal Kathleen, 2009. "A Nonlinear Mixed-Effects Model for Estimating Calibration Intervals for Unknown Concentrations in Two-Color Microarray Data with Spike-Ins," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-27, January.
    • Handle: RePEc:bpj:sagmbi:v:8:y:2009:i:1:n:5
    DOI: 10.2202/1544-6115.1401
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    Cited by:

    1. Daly Don Simone & Anderson Kevin K & Seurynck-Servoss Shannon L & Gonzalez Rachel M & White Amanda M & Zangar Richard C, 2010. "An Internal Calibration Method for Protein-Array Studies," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-23, January.
    2. Lim Johan & Kim Jayeon & Kim Byung Soo, 2010. "An Alternative Model of Type A Dependence in a Gene Set of Correlated Genes," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-12, January.

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