Pounds and Cheng (2006) describe a robust method to estimate the false discovery rate. Unlike other methods, this method is conservative when applied to one-sided or discrete p-values.
Additional details are available in the supplementary materials.
We have developed S-plus and R libraries to implement the method. To receive alerts regarding software updates, send an e-mail with "Software Update" in the subject line.
This User's Guide may be helpful in getting started.
More questions? Contact Stan Pounds.