Despite the widespread usage of DNA microarrays, questions remain about how best to interpret the wealth of gene-by-gene transcriptional levels that they measure. Recently, methods have been proposed which use biologically defined sets of genes in interpretation, instead of examining results gene-by-gene. Despite a serious limitation, a method based on Fishers exact test remains one of the few plausible options for gene set analysis when an experiment has few replicates, as is typically the case for prokaryotes.