I apologize to all who should not care about these esoteric Sequest details ...
I guess the important point of note is that the previous code did not calculate deltaCn value for the 2nd hit nor is there any placeholder to report that value anywhere in the pepXML. (We can calculate it and add in another attribute if it's important.) There's only 1 deltaCn value that is between top hit and first non-homologous hit, whether that's x2 or xN. There's also a deltacnstar attribute with valid values of 0/1 (true/false) to indicate if the deltacn value is between top 2 hits or between top hit and something lower down in the list. Hope that clarifies things. Henry Lam wrote: > Hi Jimmy, > > Oh no no. I know what deltaCn means for the top hit. It is the deltaCn > of the lower hits I'm changing. The deltaCn of the top hit is what you > described, x1-x2 in most cases, and x1-x(the highest non-homologous > hit). The code change I made should not change that (or at least I > thought). > > But what is the deltaCn of the second hit? (I know we don't use the > second hit at all in our pipeline, but it doesn't mean people won't.) > In the old code, it is x1-x3. In the new code, it is x2-x3. I don't > see why that doesn't make more sense. Similarly, the deltaCn of the > 3rd hit is x3-x4 in the new code, x1-x4 in the old code. > > That said, I was afraid that my code change had some unintended > consequence that maybe I failed to see. Let me spend some time > figuring this out. > > Henry > > On Mar 21, 12:21 am, Jimmy Eng <j...@systemsbiology.org> wrote: >> Henry, >> >> I'm not going to have any time in the next week or so to look in to the >> problem. But your interpretation of what deltaCn means is wrong or >> rather different than what it is meant to represent. >> >> The premise for the ad-hoc deltaCn value is to generate some number to >> quantify how different the top hit is from the next best hit. So >> deltaCn is always just the normalized xcorr for hit 2 (or hit 3 or hit >> N). For the typical case, it is just the difference between top hit and >> 2nd best hit (i.e. xcorr(2)). When there's homology in the top hits, >> deltaCn was calculated to be the difference between the top hit and >> first dis-similar hit. If that is the 3rd peptide then the output value >> should be normalized xcorr(3) and not xcorr(3)-xcorr(2). Hope that >> makes sense. If you would like a different interpretation of what >> number should go in that field, I guess we should discuss it offline >> including how it impacts PeptideProphet. But until then, I think you >> want to revert the correction you made for the next update release. >> >> - Jimmy >> >> >> >> Henry Lam wrote: >>> Hi Jimmy, >>> I made a change recently on SequestOut.cpp to retain the first deltaCn >>> (regardless of homology) in the deltacnstar field. I also corrected >>> the deltaCn of the lower hits (e.g. deltaCn of 2nd hit is now xcorr(3) >>> - xcorr(2) rather than xcorr(3)). I looked at it again today but >>> couldn't see why my changes would cause the behavior seen by Minyoung. >>> Maybe it's unrelated, but perhaps this will point you to something: >>> http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteom... >>> Henry >>> On Mar 19, 5:24 am, Jimmy Eng <j...@systemsbiology.org> wrote: >>>> The deltaCn is calculated from the first non-similar peptide compared to >>>> the top hit. Similarity is based on sequence homology and the cutoff is >>>> 75%. The homology determination is definitely not optimally calculated >>>> though but that doesn't explain your problems. >>>> Anyways, some of the deltaCn values in your examples below are >>>> definitely wrong; the only exception is example 1. Unfortunately I >>>> haven't seen that behavior in any of my results. Someone would need to >>>> see your files (out and pep.xml) to try to figure out the problem. >>>> - Jimmy >>>> Minyoung wrote: >>>>> Hi. >>>>> I wonder why deltaCn values from out file and from peptideprophet >>>>> shtml are different. >>>>> I observed the following: >>>>> 1. >>>>> when the best hit and the second best hit in a out file are very >>>>> similar (identical sequence except PTM), >>>>> shtml DeltaCn is calculated with reference to the third best hit. >>>>> example> in some out file >>>>> #1 P.C*HCCA.P deltCn=0.0000 >>>>> #2 P.CHCC*A.P deltCn=0.0046 >>>>> #3 R.HC*CCA.E deltCn=0.0558 >>>>> then, deltaCn in shtml is 0.0558. >>>>> 2. >>>>> when the second best and the third best hit are very similar, >>>>> shtml DeltaCn is calculated with the next best hit. >>>>> example> >>>>> #1 r.fqspagtealfe...@isvadsan@YSC*VYVDLKPPFGGSAPSER.L deltCn=0.0000 >>>>> #2 c.eecgkafnqstnltrhkrihtaekpykceecgkafnh...@.l deltCn=0.0028 >>>>> #3 c.eecgkafnqstnltrhkrihtaekpykceecgk...@hpxn.l deltCn=0.0220 >>>>> #4 Q.KFPKPLPQEYQYFDELSGIPAEDLPYYGGSVEIADYC*PFS.Q deltCn=0.1644 >>>>> then, deltaCn in shtml is 0.1644. >>>>> 3. >>>>> there is no sequence homology from the best hit to a reference hit, >>>>> but shtml DeltaCn is calculated with the reference hit. >>>>> example> >>>>> #1 e.qgxtdymgads...@ikr.k deltCn=0.0000 >>>>> #2 L.LC*ELLYESEFDSQLW.I deltCn=0.0296 >>>>> #3 a.ekic*eytytdie...@g.k deltCn=0.0417 >>>>> then, deltaCn in shtml is 0.0417. >>>>> 4. >>>>> when there are very small number of hits, >>>>> shtml DeltaCn is calculated with some not-shown hit. >>>>> example> >>>>> #1 I.LAXXXYEGLKEFZBCB.Z deltCn=0.0000 >>>>> #2 B.ZAQLSLM#QLYLTNKSD.N deltCn=0.3882 >>>>> The out file has only these two hits. >>>>> then, deltaCn in shtml is 1. >>>>> What is the rules for calculating shtml DeltaCn?- Hide quoted text - >>>> - Show quoted text -- Hide quoted text - >> - Show quoted text - > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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