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Reply to “Normalization procedures and detection of linkage signal in genetical-genomics experiments”

Nature Genetics volume 38, pages 856–858 (2006)Cite this article

Chesler et al. reply:

Williams et al. raise an important point concerning normalization that is not unique to 'genetical genomics' but is generic to microarray experiments. We address their comments based on (i) the conceptual and methodological grounds on which conclusions were drawn, (ii) the observed patterns of QTL concordance, (iii) the degree to which we have covered these issues in our work and (iv) a biological explanation of the apparently widespread lack of concordance among QTLs despite highly consistent patterns of expression regulation.

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Figure 1: Effect of normalization on genetic analysis of gene expression.

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Authors and Affiliations

  1. Life Sciences Division, Mammalian Genetics and Genomics Group, Oak Ridge National Laboratory, Oak Ridge, 37831, Tennessee, USA

    Elissa J Chesler

  2. Department of Cell Biology, Stem Cell Biology, University Medical Center Groningen, Groningen, 9713 AV, The Netherlands

    Leonid Bystrykh & Gerald de Haan

  3. Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Drive, San Diego, 92121, California, USA

    Michael P Cooke & Andrew Su

  4. Center for Genomics and Bioinformatics, University of Tennessee Health Science Center, 855 Monroe Ave., Memphis, 38163, Tennessee, USA

    Kenneth F Manly & Robert W Williams

Authors
  1. Elissa J Chesler
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  2. Leonid Bystrykh
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  3. Gerald de Haan
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  4. Michael P Cooke
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  6. Kenneth F Manly
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  7. Robert W Williams
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Correspondence to Elissa J Chesler.

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Chesler, E., Bystrykh, L., de Haan, G. et al. Reply to “Normalization procedures and detection of linkage signal in genetical-genomics experiments”. Nat Genet 38, 856–858 (2006). https://doi.org/10.1038/ng0806-856

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