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 <[email protected]> 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 <[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
>
> >
>
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