A modified two-sample t-test based on permutation method for large-scale data

In large-scale data, for example, analyzing microarray data, which includes hypothesis testing for equality of means in order to discover differentially expressed genes, often deals with a large number of features versus a few number of replicates. Furthermore, some genes are differentially expressed and some others not. Thus, a usual permutation method, which is applied facing these situations, estimates the p-value poorly. This is because two types of genes are mixed. To overcome this obstacle, the null permutation samples are suggested in the literatures. We propose a modified uniformly most powerful unbiased test for testing the null hypothesis.