Figure 4.

A comparison of the reliability of differential expression results returned by the GEO method, a few standard methods, and the voting method in a 1v1 sample comparison. The number of the top 50 differentially expressed genes from the master list that are found in a gene list of length 10, 50, 100, 150, 200, 250 and 300 is indicated on the y-axis. The GEO results based on a 1v1 sample are clearly superior to the 1v1 results from the local z-score method (as implemented in SNOMAD), or from the percentage difference (using percent changes relative to the mean expression), and almost comparable to the results of the 3v3 regularized t-test. The voting method combining the results improves the results to a level superior to a 3v3 regularized t-test.