title: Application of a correlation correction factor in a microarray cross-platform reproducibility study.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biostatistics, Virginia Commonwealth University, 730 East Broad St,, Richmond, VA, USA. kjarcher@vcu.edu
authors.forename: Kellie J
authors.initials: KJ
authors.lastname: Archer
authors.forename: Catherine I
authors.initials: CI
authors.lastname: Dumur
authors.forename: G Scott
authors.initials: GS
authors.lastname: Taylor
authors.forename: Michael D
authors.initials: MD
authors.lastname: Chaplin
authors.forename: Anthony
authors.initials: A
authors.lastname: Guiseppi-Elie
authors.forename: Geraldine
authors.initials: G
authors.lastname: Grant
authors.forename: Andrea
authors.initials: A
authors.lastname: Ferreira-Gonzalez
authors.forename: Carleton T
authors.initials: CT
authors.lastname: Garrett
mesh_terms: D002138:Calibration; D020869:Gene Expression Profiling / Q000706:statistics & numerical data*; D006801:Humans; D046228:Microarray Analysis / Q000295:instrumentation* / Q000379:methods*; D013223:Statistics as Topic / Q000379:methods*