Negative probabilities are output as place holders when there aren't enough IDs to estimate a valid mixture model. When PeptideProphet cannot compute a probability but based on other models thinks the ID is correct it reports it with a negative probability equal to the absolute charge. It would be helpful to know your PeptideProphet parameters to help troubleshoot the failure to report a mixture model probability.
-David On Mon, Jun 12, 2017 at 5:15 PM, Carolina < [email protected]> wrote: > Hello, > I built a library with decoys with SpectraST, and then, performed the > search of raw files also with SpectraST against that library. The results > were analyzed with peptide prophet but the probabilities are all negative, > from -2 to -7. My intention is to get a FDR on my results, and that > probability can not be right. Would you know what it might be going on? > Thanks, Carolina > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
