Dear all I would like to compare the identification rate of a set of PeptideProphet/iProphet validated results from Comet/X!Tandem, with MaxQuant's results. For MaxQuant I have PEPs. What is the fair way to compare the results with these two types of validations? At what threshold should I cut the peptideprohet/iprophet to be comparable with a PEP of say 0.1?
Is it fair if I compare a PEP=x with PepPro/iPro=1-x? One thing that I have noticed is that FDR calculated by mean(all PEPs) OR 1-mean(all PepPro), is always much less for PepPro. And one more question, what is an acceptable PepPro/iPro probability? Is there a way that I allow a higher FDR without changing the probability threshold? Thank you very much in advance. Ali -- 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.
