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updated metabo-batches example #233

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updated metabo-batches example #233

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mwalzer
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@mwalzer mwalzer commented Jul 23, 2024

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@mwalzer mwalzer mentioned this pull request Jul 23, 2024
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This was linked to issues Jul 25, 2024
Remove QC CV from markup docs #195
Closed
Update examples to mzQC v1.0 #225
Open
bittremieux
bittremieux requested changes Aug 7, 2024
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@bittremieux bittremieux self-requested a review October 18, 2024 11:18
bittremieux and others added 23 commits January 10, 2025 12:01
@bittremieux
Add meeting notes July 10
9b56b9c
@bittremieux
Add meeting notes July 24
45ae62d
@bittremieux @cbielow
Update set mzQC example (#219)
f8bed0c 
* Update set mzQC for validator

* Update set description

* Add temporary accession number

* Update example

* Fix typo

Co-authored-by: Chris Bielow <[email protected]>

* Fix protein contaminant metric

* Update the mzQC file as well

* Update the OBO version

* Updated CV term definition

---------

Co-authored-by: Chris Bielow <[email protected]>
@bittremieux
update QC metrics in mzML files example (#228)
da64a5c 
* Update set mzQC for validator

* Update set description

* Add temporary accession number

* Update example

* Update mzML example

* Add clarification about table metrics

* Update set mzQC for validator

* Update set description

* Add temporary accession number

* Update example

* Update mzML example

* Add clarification about table metrics
@cbielow @mwalzer @bittremieux
updated USI example to mzQC v1.0 (#229)
05f0ab1 
* updated USI example to mzQC v1.0

* Update USI-example.mzQC

fix validation issues

* Some editing

---------

Co-authored-by: Mathias Walzer <[email protected]>
Co-authored-by: Wout Bittremieux <[email protected]>
@bittremieux
Update example index
63e5a60
@bittremieux
Remove QC-CV (#236)
3192215
@mwalzer @bittremieux
trimmed some redundant sections
a54c743
@mwalzer @bittremieux
Moved validation info under one document
c3bbd53
@mwalzer @bittremieux
Added mzQC structure info
0e114b0
@mwalzer @bittremieux
updated readme for CV changes
736179f
@mwalzer @bittremieux
updated use-case story with a more robust (abstract) CV term use
417c030 
and corrected some typos
@nilshoffmann @bittremieux
Added link to MS-Quality-hub
b7fb28c
@mwalzer @bittremieux
added two metric sub-pages for use and request guide
ce821bf
@mwalzer @bittremieux
added mzQC in-a-nutshell page
3b2e5e9
@mwalzer @bittremieux
moved website in-a-nutshell page into intro as section
3089f84
@mwalzer @bittremieux
website updated: about page and a bit pruned contrib page
65789aa
@bittremieux
Add meeting notes August 7
8b205e6
@mwalzer @bittremieux
Update QC2 sample example (#231)
a370fb1 
* updated QC2 sample examples,
file validation fixes,
explanation corrections

* QC2 sample example markdown formatting

* Update example

* Update file names

* Spelling

* Fix duplicate file names

* Update CV version

---------

Co-authored-by: Wout Bittremieux <[email protected]>
@cbielow @bittremieux
Linkcheck on PR (#242)
a2c0443 
* Linkcheck on PR

fixes  #241

* Avoid redundant conditions

---------

Co-authored-by: Wout Bittremieux <[email protected]>
@bittremieux
Fix link check
4ed1c08
@cbielow @bittremieux
some menu cleanup -- not final
7a0cc5e
@cbielow @bittremieux
fix broken links
50d999a
bittremieux
bittremieux approved these changes Jan 10, 2025
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Ok, I messed up the git stuff a bit somehow. I don't think anything was lost, so should be fine.

@bittremieux
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One minor question. The metric in the individual runQualities is "number of identified quantification data points", whereas the PCA metric is "identified MS1 feature area principal component analysis result". So the number of data points vs feature area definitions don't fully seem to line up here?

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Issues reported by the validator:

  • Metadata labels of severity 6 and message: Run/SetQuality label is not unique in file!
  • ID based metric but no ID input file of severity 6 and message: ID based metrics present but no ID input file could be found registered in the mzQC file: run/set label =

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@mwalzer to look into resolving the discrepancy between run-level and set-level metrics.

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mwalzer commented Jan 10, 2025

Validator issue on mztab-M not included. https://github.com/MS-Quality-Hub/pymzqc/blob/457c09240156f9225ac8fd620a0e7cf3005a0aec/mzqc/SemanticCheck.py#L415

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Update examples to mzQC v1.0 Remove QC CV from markup docs
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@mwalzer @bittremieux @cbielow @nilshoffmann