Statistics
There are several analyses available under the Statistics tab among the analyses tabs in the top of the main window. Descriptive statistics produces a plot and table describing the data in the active data file, the t-tests and non-paramatric test compare differences of means between two groups, and one-way, two-way (GenEx Pro/Enterprise), and nested ANOVA (GenEx Enterprise) compare difference of means between several groups for different experimental designs.
A problem with all these tests is that they are usually done for more than one gene at a time. This gives rise to multiple testing problems. With a significance level of e.g. 5% for 10 independent tests, the risk of falsely rejecting one or more null hypotheses is not 5% but 40%. The more tests are performed, the more likely it is to falsely reject at least one null hypothesis. To keep the overall significance level at a given level, one can modify the threshold p-value to a lower value so that fewer null hypotheses are rejected. Therefore, when several genes are tested at once there is a message dialog that warns you that multiple tests are been performed and suggest a corrected threshold p-value that you should use to keep the overall significance of all tests at 5%.