False Discovery Rate for 2X2 Contingency Tables

This tool estimates the False Discovery Rate (FDR) for 2X2 Contingency Tables, based on the Fisher statistics.

Overview

When testing a large number of hypotheses, it can be helpful to
estimate or control the false discovery rate (FDR), the expected
proportion of tests called significant that are truly null. We use Fisher's exact test to calculate the exact null distribution over a set of 2X2 contingency tables.
Using these statistics we compute pooled pvalues, estimate the ratio of true nulls, and compute qvalues.

Application

We provide two versions of the application; A command line interface (FalseDiscoveryRate.exe) and a graphic user interface (FalseDiscoveryRateUI.exe). For a full description of the available options, please refer to the techincal report.

The graphic user interface supports the following options:
The command line application supports similar options. Run the program without any parameters to see the avialble options

References

Jonathan Carlson and David Heckerman and Guy Shani. False Discovery Rate for 2X2 Contingency Tables. Techincal report, Microsoft Research, 2009.

Web Version

http://research.microsoft.com/en-us/um/redmond/projects/MSCompBio/

Pre-Compiled Programs for Windows

Source Code Files

(To download see Source Code tab above)
Compiling the project requires