qvality - Nonparametric estimation of posterior error probabilities
qvality estimates q-values and posterior error probabilities directly from score distributions.
The method can be accessed via a web interface or downloaded as stand-alone executable, as a part of the percolator package.
If you use this software in your research, please citeLukas Käll, John D. Storey and William Stafford Noble
"qvality: Nonparametric estimation of q values and posterior error probabilities"
Bioinformatics, 25(7):964-966, February 2009
The nonparametric regression procedure is described in more detail in this paper:
Lukas Käll, John D. Storey and William Stafford Noble
"Nonparametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry"
Bioinformatics, 24(16):i42-i48, August 2008