Use the Statistics > Moderated t-test command to perform the Moderated t-test (see Smyth, 2004). This test is similar to the Student’s t-Test in that it is used to compare the means of gene expression values for two individual replicates or two groups of replicates for a given gene. The primary difference between the two methods is in the calculation of variance. The Student’s t-Test calculates variance from the data that is available for each gene. The Moderated t-Test uses information from all of the selected genes to calculate variance.
Selecting this test from the Statistics menu will launch the Statistics Parameters dialog where you can define the data to be included in the analysis, as well as the Multiple Testing Correction adjustment to be used.