Quantile Scores for Combining Results from Different Microarray Platforms

Due to the small number of replicates in typical gene microarray experiments, the performance of statistical inference is often unsatisfactory. In this article, we present a scoring scheme, based on quantiles, that allows researchers to combine data from different platforms. We have applied the discrete-continuous normal distribution (DISCO) using the quantile scores on two publicly available data sets. Differentially expressed genes identified by DISCO are comparable to those identified by significance analysis of microarray (SAM) or Wilcoxon rank test. An algorithm based on DISCO and quantile scores is developed to combine results from Affymetrix and Illumina. Our results indicate that combining microarray data from different platforms is possible and straightforward. AVAILABILITY: R code implementing our methods is available from the authors.