=== Fisher's exact test === * For experiments without replication * Fisher's exact test can be used on a 2x2 (or larger) contingency matrix to test dependency between rows and columns * For expression counts, the 4 values are * number of counts for Gene A in Sample 1 * number of counts not for Gene A in Sample 1 * number of counts for Gene A in Sample 2 * number of counts not for Gene A in Sample 2 * A test is performed for every gene of interest. * This was a popular method in earlier SAGE expression counts and is also tested in [[http://www.ncbi.nlm.nih.gov/pubmed/20167110|Bullard et al., 2010]]. * We don't yet have a command-line script to perform this on 2 samples, followed by FDR correction. * As with any method not taking advantage of biological replication, any conclusions must be treated with care (and not taken too seriously).