Hi David Thanks for the reply. When I exported the PeptideProphet results and compared 'Phenyx zscore' to fvalue, the transformation did not appear to be linear. For around 20% of peptides, the (fvalue = zcore - 4) but for the others there was a large amount of scatter and the relationship appeared much more complex. Of course, this has a major effect on the calculated probabilities vs. if zscore was used. Any further advice would be much appreciated!
Many thanks Matt On May 27, 7:39 pm, David Shteynberg <[email protected]> wrote: > 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 > > athttp://groups.google.com/group/spctools-discuss?hl=en.- Hide quoted text - > > - Show quoted text - -- 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.
