J-Express pro now include the following methods to test for differential expression between two microarray experiment states:
t-score
The t-score is the two sample t-statistic. Given means of two experiment classes m1 and m2, the pooled standard deviation estimate sp, and the number of experiments in each class n1 and n2, the score is computed by the formula
Golub score
The Golub score is named after the widely referenced paper by Golub et al. [3]. This scoring method is often referred to as the “signal-to-noise” ratio. Given means of two experiment conditions m1 and m2 and the corresponding standard deviations s1 and s2, the score value is computed by the formula
Between/within variance ratio
The between-to-within variance ratio reflects differences in class means relative to the variances in the classes. This score method was introduced by Dudoit et al. [2]. Given the class means m1 and m2, the grand mean 
and the within class sum of squares ss1 and ss2 the score is computed by the formula
Wilcoxon z-approximation
The Wilcoxon z-approximation is a nonparametric score based on the Wilcoxon rank sum statistic. Given a decent number of experiments, the score is approximately standard normal distributed. The expression values are ranked and the rank sum Wa of the smaller sample size is computed. Given the number of experiments in the smaller class na and in the larger class nb (na ≤ nb), the score is computed by the formula.
For further details, see for instance Bhattacharyya and Johnson [1].
[1] Bhattacharyya GK and Johnson RA: Statistical concepts and methods. Wiley, 1977.
[2] Dudoit S, Fridlyand J, Speed T: Comparison of discrimination methods for the classification of tumors using gene expression data. Technical report no. 576, Department of Statistics, University of California, 2000.
[3] Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeeck M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al.: Molecular classi_cation of cancer: Class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537.