Bill, If you're interested in Tandem's E-value , there is an option that David added in a long time ago that allows the Tandem's E-value to be used in place of the discriminant function. The xinteract option to invoke this is "-OE". Looks like this adds "EXPECTSCORE" to the PeptideProphetParser command line.
On Wed, Sep 16, 2009 at 5:52 AM, Brendan <[email protected]> wrote: > > 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 -~----------~----~----~----~------~----~------~--~---
