Select a data set and desirable parameters to analyze. FDR is typically set at 0.05 and Permutation number at around 500.

False discovery rate:
False discovery rate is used in the Kruskal-Wallis procedure for selecting differentially expressed genes.

Number of permutations
Data are permuted using a Monte Carlo method used by the Kruskal-Wallis procedure to compensate for a small number of replicates. A small number (e.g. 100) will produce results quickly whereas a large number (e.g. 1000) will take much more time (but with more reliable results).