Runs the specified test, and returns the genes that have a corrected p-value smaller than the specified p-value cut-off. If you want to get a p-value for every single gene in your data set, set the p-value cut-off to 1. This should return a new gene list of equal length to the original one.
Multiple testing correction options are Bonferroni, Holm, and Hochberg for family-wise error rate (FWER) and Benjamini-Hochberg and Benjamini-Yakutieri for false discovery rate (FDR). Of these Bonferroni is the most conservative, returning the smallest number of significant results, and FDR-based adjustments are less conservative, and return more significant results.
This tool uses Bioconductor package limma. Please cite the following articles, if you used empirical Bayes:
Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Ge- netics and Molecular Biology, Vol. 3, No. 1, Article 3.