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A Novel and Fast Normalization Method for High-Density Arrays

Author

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  • van Iterson Maarten

    (Center for Human and Clinical Genetics, Leiden University Medical Center)

  • Duijkers Floor A.M.

    (Department of Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital)

  • Meijerink Jules P.P.

    (Department of Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital)

  • Admiraal Pieter

    (Department of Pediatric Oncology/Hematology, Erasmus University Medical Center-Sophia Children's Hospital)

  • van Ommen Gert-Jan B.

    (Center for Human and Clinical Genetics, Leiden University Medical)

  • Boer Judith M.
  • van Noesel Max M.
  • Menezes Renee X.

Abstract

Background: Among the most commonly applied microarray normalization methods are intensity-dependent normalization methods such as lowess or loess algorithms. Their computational complexity makes them slow and thus less suitable for normalization of large datasets. Current implementations try to circumvent this problem by using a random subset of the data for normalization, but the impact of this modification has not been previously assessed. We developed a novel intensity-dependent normalization method for microarrays that is fast, simple and can include weighing of observations.

Suggested Citation

  • van Iterson Maarten & Duijkers Floor A.M. & Meijerink Jules P.P. & Admiraal Pieter & van Ommen Gert-Jan B. & Boer Judith M. & van Noesel Max M. & Menezes Renee X., 2012. "A Novel and Fast Normalization Method for High-Density Arrays," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(4), pages 1-31, July.
    • Handle: RePEc:bpj:sagmbi:v:11:y:2012:i:4:n:5
    DOI: 10.1515/1544-6115.1753
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    References listed on IDEAS

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    1. Ruppert,David & Wand,M. P. & Carroll,R. J., 2003. "Semiparametric Regression," Cambridge Books, Cambridge University Press, number 9780521785167.
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    3. Ruppert,David & Wand,M. P. & Carroll,R. J., 2003. "Semiparametric Regression," Cambridge Books, Cambridge University Press, number 9780521780506.
    4. Inyoung Kim & Noah D. Cohen & Raymond J. Carroll, 2003. "Semiparametric Regression Splines in Matched Case-Control Studies," Biometrics, The International Biometric Society, vol. 59(4), pages 1158-1169, December.
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