Application of a correlation correction factor in a microarray cross-platform reproducibility study

Kellie J. Archer, Catherine I. Dumur, G. Scott Taylor, Michael D. Chaplin, Anthony Guiseppi-Elie, Geraldine Grant, Andrea Ferreira-Gonzalez, Carleton T. Garrett

Research output: Contribution to journalArticle

5 Scopus citations

Abstract

Background: Recent research examining cross-platform correlation of gene expression intensities has yielded mixed results. In this study, we demonstrate use of a correction factor for estimating cross-platform correlations. Results: In this paper, three technical replicate microarrays were hybridized to each of three platforms. The three platforms were then analyzed to assess both intra- and cross-platform reproducibility. We present various methods for examining intra-platform reproducibility. We also examine cross-platform reproducibility using Pearson's correlation. Additionally, we previously developed a correction factor for Pearson's correlation which is applicable when X and Y are measured with error. Herein we demonstrate that correcting for measurement error by estimating the "disattenuated" correlation substantially improves cross-platform correlations. Conclusion: When estimating cross-platform correlation, it is essential to thoroughly evaluate intra-platform reproducibility as a first step. In addition, since measurement error is present in microarray gene expression data, methods to correct for attenuation are useful in decreasing the bias in cross-platform correlation estimates.

Original languageEnglish (US)
Article number447
JournalBMC bioinformatics
Volume8
DOIs
StatePublished - Nov 15 2007

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

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