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Highly efficient factorial designs for cDNA microarray experiments: use of approximate theory together with a step-up step-down procedure

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  • Zhang Runchu

    (KLAS and School of Mathematics and Statistics, Northeast Normal University, Changchun 130024, China Department of Statistics, The University of British Columbia, BC, V6T 1Z4 Canada LPMC and School of Mathematical Sciences, Nankai University, Tianjin 300071, China)

  • Mukerjee Rahul

    (Indian Institute of Management Calcutta, Joka, Diamond Harbour Road, Kolkata 700 104, India)

Abstract

A general method for obtaining highly efficient factorial designs of relatively small sizes is developed for cDNA microarray experiments. It allows the main effects and interactions to be of possibly unequal importance. First, the approximate theory is employed to get an optimal design measure which is then discretized. It is, however, observed that a naïve discretization may fail to yield an exact design of the stipulated size and, even when it yields such an exact design, there is often scope for improvement in efficiency. To address these issues, we propose a step-up/down procedure which is seen to work very well. The resulting designs turn out to be quite robust to possible dye-color effects and heteroscedasticity. We focus on the baseline and all-to-next parametrizations but our method works equally well also for hybrids of the two and other parametrizations.

Suggested Citation

  • Zhang Runchu & Mukerjee Rahul, 2013. "Highly efficient factorial designs for cDNA microarray experiments: use of approximate theory together with a step-up step-down procedure," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 12(4), pages 489-503, August.
    • Handle: RePEc:bpj:sagmbi:v:12:y:2013:i:4:p:489-503:n:5
    DOI: 10.1515/sagmb-2012-0054
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    References listed on IDEAS

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    1. M. Kathleen Kerr, 2003. "Design Considerations for Efficient and Effective Microarray Studies," Biometrics, The International Biometric Society, vol. 59(4), pages 822-828, December.
    2. Kerr Kathleen F., 2012. "Optimality Criteria for the Design of 2-Color Microarray Studies," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(1), pages 1-9, January.
    3. Landgrebe, Jobst & Bretz, Frank & Brunner, Edgar, 2006. "Efficient design and analysis of two colour factorial microarray experiments," Computational Statistics & Data Analysis, Elsevier, vol. 50(2), pages 499-517, January.
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