Hi Bill, I am the one who wrote it several years back. I derived the fval somewhat by voodoo, using analysis tools I created in CPAS. It tested quite well, and if anything produces slightly conservative probabilities, where I felt the k-score fval was slightly optimistic in its estimates (but only slightly). Note that the k-score fval was derived for the scoring function originally published by Keller, et al, before the score was incorporated into X! Tandem, and therefore makes no use of X! Tandem's expect value.
These fval calculations can be found in <tpproot>/src/Validation/ DiscriminateFunction/Tandem (for native scoring) and Comet (for k- score). I remember that a peptide length correction (I think sqrt(length) actually) was important in the final native fval. Because of how aggressively X! Tandem weights the presence of matching ions, a larger peptide is more likely to produce a wider spread between its best and second best score, the key factor in the expectation value. Hope that helps. --Brendan On Sep 15, 2:30 pm, bill <[email protected]> wrote: > If this is not easily available can you direct me to the class/script/ > method that creates the xtandem fval? > Thanks, > Bill > > On Sep 14, 4:16 pm, Bill Nelson <[email protected]> wrote: > > > Can you please explain how ProteinProphet calculates the fval from the > > xtandem output? > > It doesn't seem to be tracking the xtandem E-value, what else is > > included? > > Thanks, > > Bill --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
