Three methodologies are implemented in Babelomics. The method proposed by Holm controls the FWER (family-wise error rate). The other two methods control the FDR (false discovery rate). One of them uses the algorithm proposed by Benjamini & Hochberg and the other one implements the q-values method proposed by Storey. Our implementations make use of the p.adjust function in the stats R package and the qvalues package from Bioconductor.