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

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.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.Previous microarray gene expression studies have examined within-platform reproducibility among different generations of the Affymetrix GeneChip [1,2] and among cDNA-based array platforms [3,4]. Subsequently, several cross-platform reproducibility studies have been reported, many of which examined either the consistency of intensities or the consistency with which different platforms identify genes significantly differently expressed [5-18]. Results from another large cross-platform study, the MicroArray Quality Control (MAQC) project, led by the US Food and Drug Administration with 51 participating universities and major biotechnology companies, have also been reported [19-24]. Some of these early studies demonstrated poor cross-platform correlations. For example, among 384 genes commonly declared present in a cDNA-based microarray and the Affymetrix HG-U95Av2 GeneChip platform, the Spearman correlation was only 0.131. Other cross-platform studies also reported low cross-platform correlations [5,8]. In addition, in a