Use direct experiments to find genes that are significantly changed between two samples (A and B).
1. If the experiments are repeated, calculate the average of the log2 of the expression ratio for each repeat.
2. For an estimate of the error in measurement for each specific gene, use the table listing the global standard errors.
3. Use a t-test to determine whether your measured change in gene expression (calculated in 1) is significant, given the error (shown in 2) and the number of experimental repeats.