This review compares different methods to identify differentially expressed genes in two-sample cDNA arrays. A two-sample experiment is a commonly used design to compare relative mRNA abundance between two different samples. This simple design is customarily used by biologists as a first screening before relying on more complex designs. Statistical techniques are quite well developed for such simple designs. For the identification of differentially expressed genes, four methods were described and compared: a fold test, a t-test (Long et al., 2001), SAM (Tusher et al., 2001) and an ANOVA-based bootstrap method (Kerr and Churchill, 2001). Mutual comparison of these methods clearly illustrates each method's advantages and pitfalls. Our analyses showed that the most reliable predictions are made by the combined use of different methods, each of which is based on a different statistic. The ANOVA-based bootstap method used in this study performed rather poorly in identifying differentially expressed genes.
