Many researchers have used the intersection method to compare the results of differential expression analysis between two or more gene expression experiments. Some methods have been proposed to estimate the number of genes commonly differentially expressed in two independent gene expression experiments or analyses, but there has not been a method for estimating this number using dependent experiments or analyses other than the intersection method. In this thesis project, we propose a method for estimating the number of differentially expressed genes in two dependent experiments or analyses. Simulation studies are performed to compare the proposed to existing methods and an analysis of a real gene expression data set is performed to illustrate the use of the proposed method.