Detecting Differential Expressions in GeneChip Microarray Studies

In this article we consider testing for differentially expressed genes in GeneChip studies by modeling and analyzing the quantiles of gene expression through probe level measurements. By developing a robust rank score test for linear quantile models with a random effect, we propose a reliable test for detecting differences in certain quantiles of the intensity distributions. By using a genomewide adjustment to the test statistic to account for within-array correlation, we demonstrate that the proposed rank score test is highly effective even when the number of arrays is small. Our empirical studies with real experimental data show that detecting differences in the quartiles for the probe level data is a valuable complement to the usual mixed model analysis based on Gaussian likelihood. The methodology proposed in this article is a first attempt to develop inferential tools for quantile regression in mixed models.