Hi Jimmy and Bill, I am sure using EXPECTSCORE in place of the fval has received less testing for the veracity of its probabilities, something Alexei was adamant about when I developed the fval for the X! Tandem native score. You have to run searches with decoys and look at q-q plots for this. Also, Alexei was initially dubious whether PeptideProphet would work at all on X! Tandem native, because the expect scoring distribution has a significant left skew, and is far from normal, which I believe I was able to mitigate somewhat with the variables I added in the fval. And, finally, my own ROC plots showed this fval doing a better job at discriminating between true- and false-positive hits.
So, go cautiously into throwing that switch, and make your own estimations of benefit v. cost. --Brendan On Sep 16, 9:36 am, Jimmy Eng <[email protected]> wrote: > 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 -~----------~----~----~----~------~----~------~--~---
