Thanks for your help. My next step was to run it in a debugger but I
don't have a visual studio license. I hate to do it but I guess I'll
have to give Microsoft more money.I'll post the results if I figure it
out.
Bill
On Oct 6, 8:44 am, Brendan <brend...@proteinms.net> wrote:
> Hi Bill,
> I think you are going to have to build it yourself, and do some printf
> debugging to get yourself through this one. I looked over what you
> wrote, and the only issue I can see is that next_score appears to be
> 221 and not 210, but that only makes the final value further from what
> is reported.
>
> At this point I'd start having the code print out values for me to
> check my assumptions. I am afraid I can't help you with that, though.
>
> By the way, I can't take any credit for the k-score discriminant
> function. It is the same function created for the original Keller
> OMICS paper where the score was introduced, and mimics Comet
> discriminant score. I created the discriminant score for X! Tandem
> native scoring.
>
> The expect_wt_ and len_wt_ values are initialize to zero in the
> TandemDiscrimFunction base class.
>
> --Brendan
>
> On Oct 5, 12:19 pm, bill <nelson...@gmail.com> wrote:
>
>
>
> > Thanks again for the feedback! We compared plain old expect values to
> > those with the Brendan's discriminant scoring and our samples
> > performed better with Brendan's scoring. So, now I'm back to figuring
> > out how fval is calculated.
>
> > I'm trying to maually work through calculating the fval for an xtandem
> > (k-score) result.
>
> > My stripped down pep.xml entry looks like this:
>
> > <spectrum_query spectrum="010319_f16.00923.00923.1"
> > <search_result>
> > <search_hit hit_rank="1" peptide="AISDAMFANPK" >
> > <search_score name="hyperscore" value="253"/>
> > <search_score name="nextscore" value="221"/>
> > <search_score name="expect" value="0.79"/>
> > <analysis_result analysis="peptideprophet">
> > <peptideprophet_result probability="0.1732"
> > all_ntt_prob="(0.0000,0.0000,0.1732)">
> > <search_score_summary>
> > <parameter name="fval" value="1.0108"/>
>
> > I'm plugging the values into the getDiscriminantScore method in
> > TandemDiscrimFunction:
>
> > double TandemDiscrimFunction::getDiscriminantScore(SearchResult*
> > result)
> > {
> > TandemResult* tresult = (TandemResult*)(result);
> > double tot = const_;
> > double disc = score_wt_ * log((double)tresult->hyper_) + expect_wt_
> > * (0-log((double)tresult->expect_)) + delta_wt_ * (1.0 - (tresult->next_ /
> > tresult->hyper_));
>
> > if (len_wt_)
> > disc /= len_wt_ * sqrt((double)strlen(tresult->peptide_));
> > tot += disc;
> > if (use_expect_) {
> > tot = 3 * tot - 8;
> > }
> > return tot;
>
> > }
>
> > I'm initailizing through TandemKscoreDF.cxx with TandemKscoreDF(1,
> > false)
>
> > static double consts[] = {-13.287, -28.708, -31.083, -31.083,
> > -31.083};
> > static double score_wts[] = {2.256, 4.91, 4.983, 4.983, 4.983};
> > static double delta_wts[] = {14.346, 10.882, 18.091, 18.091, 18.091};
>
> > if (!use_expect)
> > {
> > const_ = consts[charge];
> > score_wt_ = score_wts[charge];
> > delta_wt_ = delta_wts[charge];
>
> > }
>
> > So my manual calculation looks like this:
> > tot = -28.708
> > disc = 4.91 * ln(253) + 0 * (0 - ln(0.79)) + 10.882 * (1.0 -
> > (210/253)) =
> > 4.91 * 5.533 + 0 * 0.236 + 10.882 * 0.169 =
> > 27.169 + 0 + 1.8495 =
> > 29.185
>
> > tot = -28.708 + 29.185 = 0.311
>
> > But, I'm trying to reproduce the fval of 1.0108. I'm not an
> > experienced C++ programmer. Am I missing where expect_wt_ and len_wt_
> > are initaillized? Is ther another step to the calculation?
>
> > Thanks,
> > Bill
>
> > On Sep 17, 1:05 pm, David Shteynberg <dshteynb...@systemsbiology.org>
> > wrote:
>
> > > The EXPECTSCORE option was something that was added after f-val at
> > > Alexey request. I believe the reason for the inclusion of this option
> > > is in the usage statement:
>
> > > E [only use Expect Score as the Discriminant(applies only to X!Tandem
> > > data,
> > > helpful for data with homologous top hits e.g. phospho or glyco)]
>
> > > -David
>
> > > On Thu, Sep 17, 2009 at 4:54 AM, Brendan <brend...@proteinms.net> wrote:
>
> > > > 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 <jke...@gmail.com> 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 <brend...@proteinms.net>
> > > >> 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 <nelson...@gmail.com> 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 <nelson...@gmail.com> 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
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