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Combining Multiple Laser Scans of Spotted Microarrays by Means of a Two-Way ANOVA Model

Author

Listed:
  • Ambroise Jérôme

    (Université catholique de Louvain)

  • Bearzatto Bertrand

    (Université catholique de Louvain)

  • Robert Annie

    (Université catholique de Louvain)

  • Macq Benoit

    (Université catholique de Louvain)

  • Gala Jean-Luc

    (Université catholique de Louvain)

Abstract

Motivation: Assessment of gene expression on spotted microarrays is based on measurement of fluorescence intensity emitted by hybridized spots. Unfortunately, quantifying fluorescence intensity from hybridized spots does not always correctly reflect gene expression level. Low gene expression levels produce low fluorescence intensities which tend to be confounded with the local background while high gene expression levels produce high fluorescence intensities which rapidly reach the saturation level. Most algorithms that combine data acquired at different voltages of the photomultiplier tube (PMT) assume that a change in scanner setting transforms the intensity measurements by a multiplicative constant.Methods and Results: In this paper we introduce a new model of spot foreground intensity which integrates a PMT voltage independent scanner optical bias. This new model is used to implement a ”Combining Multiple Scan using a Two-way ANOVA” (CMS2A) method, which is based on a maximum likelihood estimation of the scanner optical bias. After having computed scanner bias, coefficients of the two-way ANOVA model are used for correcting the saturated spots intensities obtained at high PMT voltage by using their counterpart values at lower PMT voltages. The method was compared to state-of-the-art multiple scan algorithms, using data generated from the MAQC study. CMS2A produced fold-changes that were highly correlated with qPCR fold-changes. As the scanner optical bias is accurately estimated within CMS2A, this method allows also avoiding fold-change compression biases whatever the value of this optical bias.

Suggested Citation

  • Ambroise Jérôme & Bearzatto Bertrand & Robert Annie & Macq Benoit & Gala Jean-Luc, 2012. "Combining Multiple Laser Scans of Spotted Microarrays by Means of a Two-Way ANOVA Model," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(3), pages 1-20, February.
    • Handle: RePEc:bpj:sagmbi:v:11:y:2012:i:3:n:8
    DOI: 10.1515/1544-6115.1738
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    References listed on IDEAS

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    1. Gupta Rashi & Auvinen Petri & Thomas Andrew & Arjas Elja, 2006. "Bayesian Hierarchical Model for Correcting Signal Saturation in Microarrays Using Pixel Intensities," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 5(1), pages 1-20, August.
    2. Smyth Gordon K, 2004. "Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 3(1), pages 1-28, February.
    3. Ambroise, Jerome & Bearzatto, Bertrand & Robert, Annie & Govaerts, Bernadette & Macq, Benoit & Gala, Jean-Luc, 2011. "Impact of the spotted microarray preprocessing method on fold-change compression and variance stability," LIDAM Reprints ISBA 2011054, Université catholique de Louvain, Institute of Statistics, Biostatistics and Actuarial Sciences (ISBA).
    4. Cui Xiangqin & Kerr M. Kathleen & Churchill Gary A., 2003. "Transformations for cDNA Microarray Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 2(1), pages 1-22, June.
    5. García de la Nava Jorge & van Hijum Sacha & Trelles Oswaldo, 2004. "Saturation and Quantization Reduction in Microarray Experiments using Two Scans at Different Sensitivities," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 3(1), pages 1-18, June.
    6. Huber Wolfgang & von Heydebreck Anja & Sueltmann Holger & Poustka Annemarie & Vingron Martin, 2003. "Parameter estimation for the calibration and variance stabilization of microarray data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 2(1), pages 1-24, April.
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