Gene expression data from microarray experiments have been studied using several statistical models. Significance Analysis of Microarrays (SAM), for example, has proved to be useful in analyzing microarray data. In the spirit of the SAM procedures, we develop permutation based rank-tests for generalized Wilcoxon ranksum test for two-group comparisons of replicated microarray data. Also, for microarray experiments with randomized block design, we consider generalized signed rank test. The statistical analysis software package is written in R and is freely available in a package.