Both microarray and RNA-seq technologies are powerful tools which are commonly used in differential expression (DE) analysis. Gene expression levels are compared across treatment groups to determine which genes are differentially expressed. With both technologies, filtering and normalization are important steps in data analysis. In this thesis, real datasets are used to compare current analysis methods of two-color microarray and RNA-seq experiments. A variety of filtering, normalization and statistical approaches are evaluated. The results of this study show that although there is still no widely accepted method for the analysis of these types of experiments, the method chosen can largely impact the number of genes that are declared to be differentially expressed.