Figure 3

A comparison of the reliability of differential expression results returned by regularized t-test, the GEO method and the voting method in a 2v2 sample comparison. The number of the top 50 differentially expressed genes from the master list that are found in the gene list of length 10, 50, 100, 150, 200, 250 and 300 is indicated on the y-axis. The GEO results based on a 2v2 sample are clearly superior to the 2v2 regularized t-test results, and roughly comparable to the results of the 3v3. The voting method combining the results improves the results to a level almost comparable to a 4v4 regularized t-test.