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oddities in output #6
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Looks like you found a bug in errorcalc.py, on line 254. As you noted, it appears to be giving you the same number of spectra that it's able to use for every charge. What it's actually reporting is the total number of usable spectra across all charges. I believe I could fix the bug very easily by changing line 254 to report However, it's been a long time since I looked at this code, and I'm a little nervous about screwing it up. So, two options for you:
I'll try to get around to fixing it, but verifying the fix would take me far longer than making it. If I made the fix on a branch, would you be willing check out the branch and verify it for me? If so, I'll update this issue when it's done on a branch. |
Thanks for the quick response.
which looks more reasonable. But the largest reported number there is 850 which is not the number of peak pairs, 189. Is that because 850 represents the total number of paired spectra, not the number of peak pairs? |
Ha, that's what I get for trying to barge back into code I haven't looked at in years. I gave you the wrong variable to plug in there. Try it with |
Haha. At least the code is nice and readable! I'll give that a try.
…On Wed, Apr 22, 2020 at 4:25 PM Damon May ***@***.***> wrote:
Ha, that's what I get for trying to barge back into code I haven't looked
at in years. I gave you the wrong variable to plug in there. Try it with
len(percharge_calculator.paired_precursor_mzs).
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Okay, this looks good now! Here is the output this time:
The numbers for charge 2, 3 and 4 add up to the reported number of peak pairs (189). Charge 0 doesn't seem to be contributing to the number of peak pairs. Are unknown charges not used? |
Hello,
Thanks for making this tool! I am finding it useful and am planning to use it in a large-scale reanalysis of published data to avoid difficulties with missing/incomplete information on acquisition parameters.
I noticed something that seems odd about the output and am wondering if you can help clarify it. Here are the details of an analysis of some data from a sciex triple tof:
All these numbers make sense to me except
and also with sufficient in-common fragments:
, which is exactly the same for each charge state. Is this expected?Also, when I run the same file and specify
--charges 2
then this is the output:The numbers match charge 2 from above except now
sufficient in-common fragments
is different. Is this expected?Also, I'm aware that I'm seeing these detail reports because there are not enough paired spectra to do the analysis. But I would still like to understand the output here.
Best,
Kevin
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