Gaussian-based tests
The tests based on the Gaussian distribution essentially compare the mean expression level in the experimental groups in the study, and evaluates the significance of the difference relative to the variance (or 'spread') of the data within the groups. The details of the formula used for calculating the test statistics vary according to the experimental setup and the assumptions you make about the data (read more about this in the sections on t-test and ANOVA below). The explanation of how to proceed is divided into two, depending on how many groups there are in your experiment. First comes the explanation for t-tests which is the only analysis available for two-group experimental setups (t-tests can also be used for pairwise comparison of groups in multi-group experiments). Next comes an explanation of the ANOVA test which can be used for multi-group experiments.
Note that the test statistics for the t-test and ANOVA analysis use the estimated group variances in their denominators. If all expression values in a group are identical the estimated variance for that group will be zero. If the estimated variances for both (or all) groups are zero the denominator of the test statistic will be zero. The numerator's value depends on the difference of the group means. If this is zero, the numerator is zero and the test statistic will be 0/0 which is NaN. If the numerator is different from zero the test statistic will be + or - infinity, depending on which group mean is bigger. If all values in all groups are identical the test statistic is set to zero.
Subsections