Data and Text Mining A Note on the False Discovery Rate and Inconsistent Comparisons between Experiments.

Motivation: The false discovery rate (FDR) has been widely adopted to address the multiple comparisons issue in high through-put experiments such as microarray gene expression studies. How-ever, while the FDR is quite useful as an approach to limit false discoveries within a single experiment, like other multiple compari-son corrections it may be an inappropriate way to compare results across experiments. This paper uses several examples based on gene expression data to demonstrate the potential misinterpretations that can arise from using FDR to compare across experiments. Researchers should be aware of these pitfalls and wary of using FDR to compare experimental results. FDR should be augmented with other meas-ures such as p-values and expression ratios. It is worth including standard error and variance information for meta-analyses and, if possible, the raw data for re-analyses. This is especially important for high throughput studies because data are often reused for differ-ent objectives, including comparing common elements across many experiments. No single error rate or data summary may be appro-priate for all of the different objectives.