The message is just a warning since this work has not been "peer reviewed" in the form of a journal aritcle. It suggests you might want to have a second opinion in the FDR being computed directly from the probabilities generated, for instance by including decoys in your search. In fact the favlue is just a linear transformation of the native search scores so the two should be interchangeable.
-David On Thu, May 27, 2010 at 2:51 AM, MattK <[email protected]> wrote: > Hello all > > I noticed when I used PeptideProphet on Phenyx results (exported as > pepxml) that there is a warning issued by TPP that the Phenyx fvalue > calculation is new and untested/unreliable. Is there any way to force > PeptideProphet to use native db search scores and not fvalues? > > Thanks, > > MattK > > using TPP v4.3 JETSTREAM rev 0, Build 200908071234 (MinGW) > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
