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de Andrade M, Atkinson EJ, Fridley BL, et al. The genetics of gene expression: comparison of linkage scans using two phenotype normalization methods. BMC Proc. 2007;1:S151doi: 10.1186/1753-6561-1-s1-s151.
de Andrade, M., Atkinson, E. J., Fridley, B. L., Goode, E. L., McDonnell, S., Liu-Mares, W., Rabe, K. G., Sun, Z., & Slager, S. L. (2007). The genetics of gene expression: comparison of linkage scans using two phenotype normalization methods. BMC proceedings, 1S151. https://doi.org/10.1186/1753-6561-1-s1-s151
de Andrade, Mariza, et al. "The genetics of gene expression: comparison of linkage scans using two phenotype normalization methods." BMC proceedings vol. 1 (2007): S151. doi: https://doi.org/10.1186/1753-6561-1-s1-s151
de Andrade M, Atkinson EJ, Fridley BL, Goode EL, McDonnell S, Liu-Mares W, Rabe KG, Sun Z, Slager SL. The genetics of gene expression: comparison of linkage scans using two phenotype normalization methods. BMC Proc. 2007;1:S151. doi: 10.1186/1753-6561-1-s1-s151. Epub 2007 Dec 18. PMID: 18466496; PMCID: PMC2367553.
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BMC Proc. 2007;1:S151. doi: 10.1186/1753-6561-1-s1-s151. Epub 2007 Dec 18.

The genetics of gene expression: comparison of linkage scans using two phenotype normalization methods.

BMC proceedings

Mariza de Andrade, Elizabeth J Atkinson, Brooke L Fridley, Ellen L Goode, Shannon McDonnell, Wen Liu-Mares, Kari G Rabe, Zhifu Sun, Susan L Slager

Affiliations

  1. Division of Biostatistics, Mayo Clinic College of Medicine, 200 First Street Southwest, Harwick 7, Rochester, Minnesota 55905, USA. [email protected]

PMID: 18466496 PMCID: PMC2367553 DOI: 10.1186/1753-6561-1-s1-s151

Abstract

The goal of this paper is to investigate the effects of normalization procedures for expression data on linkage results. We selected the two most commonly used expression data extraction and normalization methods, Affymetrix global scaling and dChip invariant. After applying these two methods in 3554 expression phenotypes, we identified 45 phenotypes that were more likely to be genetic for either normalization procedure. A genome-wide linkage scan was performed on these expression values (45 phenotypes x 2 normalizations) using 2272 SNPs. Our results showed that: 1) the dChip normalization might inflate the LOD scores because the dChip normalization yielded LOD scores > 3.0 30% more frequently than the Affy normalization, and 2) the difference in LODs between the normalizations were not correlated with their heritabilities. In summary, we conclude, as have other published reports, that normalization methods play an important role in the linkage results, and that some significant linkage signals might be due to a specific normalization method.

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