Importance of presenting the variability of the false discovery rate control

BACKGROUND: Multiple hypothesis testing is a pervasive problem in genomic data analysis. The conventional Bonferroni method which controls the family-wise error rate is conservative and with low power. The current paradigm is to control the false discovery rate. RESULTS: We characterize the variability of the false discovery rate indices (local false discovery rates, q-value and false discovery proportion) using the bootstrapped method. A colon cancer gene-expression data and a visual refractive errors genome-wide association study data are analyzed as demonstration. We found a high variability in false discovery rate controls for typical genomic studies. CONCLUSIONS: We advise researchers to present the bootstrapped standard errors alongside with the false discovery rate indices. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-015-0259-z) contains supplementary material, which is available to authorized users.