How can BRB-ArrayTools help manage false discoveries?
You can specify limits for the number of false discoveries or the proportion of false discoveries. Multivariate permutation tests are used to find the genes meeting the specified criteria. The multivariate permutation tests are based on permutations of the labels of which arrays are in which classes. A large number of random permutations are considered. For each random permutation, the parametric tests are re-computed to determine a p value for each gene that is a measure of the extent it appears differentially expressed between the random classes determined by the random permutation. The genes are ordered by their p values computed for the random permutation (genes with smallest p values at the top of the list). For each potential p value threshold, the program records the number of genes in the list. This process is repeated for a large number of random permutations. Consequently, for any p value threshold, we can compute the distribution of the number of genes that would have p valu
