Deay Henry,
I really appreciate all your comments.
The IDs for case 3 and 4 were really the 2nd hit.
Now all make sense to me.
I agree with your points and hope the work will be done well.
Minyoung.
On 3월23일, 오후2시01분, Henry Lam wrote:
> Dear Minyoung,
>
> Thanks for your message. Did you manag
Dear Minyoung,
Thanks for your message. Did you manage to check the actual IDs for
Cases 3 and 4? I suppose if our X filter is working properly, then
your IDs should be the second hits, not the top hits any more.
In Case 4, if the top hit is thrown out, then the second hit is the
only hit. In su
Hi Henry,
Sorry for late reply.
I used Petunia, and made pepXML with default setting.
I checked the amino acid X problem, and confirmed your comment.
In addition, when the best hit has the X, the shtml deltaCn was
calculated from delow the 3rd hit even though the 2nd hit does not
contain X. The 3
Dear Minyoung,
I think I found the issue. It does not have anything to do with the
calculation of deltaCn values, but the fact that in Minyoung's
examples, some of the lower hits have the "amino acid" X in it. The
default behavior of the .out to .pep.xml converter is that all X-
containing peptid
Hi Minyoung,
I have trouble reproducing your results from here. Would you help me
by telling me how exactly you come up with the .out files and .pep.xml
files that show the anomaly? i.e. the exact command you run? Perhaps
even copy and paste the out files and the portion of .pep.xml file for
me?
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
a
Hi Jimmy and Minyoung,
Mm... on longer look, something is fishy. In any case, I will revert
the code changes first while I fix this. This thing's on me.
Minyoung, thanks for catching this.
Henry
On Mar 21, 7:42 am, Henry Lam wrote:
> Hi Jimmy,
>
> Oh no no. I know what deltaCn means for the t
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).
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
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
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
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