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Lod tutorial documentation #364

Merged
merged 21 commits into from
May 30, 2024
Merged

Lod tutorial documentation #364

merged 21 commits into from
May 30, 2024

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kristynchin-olink
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Title: Write a very short summary here

Problem: Write a description of your problem here.

Solution: Write a short summary of your solution.

Key Features:

  • Key feature 1
  • Key feature 2
  • ...

Checklist

  • Make sure you are requesting to pull a feature/bugfix branch (right side). This should not be main or develop.
  • Make sure you are make a pull request against either main or develop (left side). (Requesting to main should be reserved for bugfixes and new releases)
  • Add or update unit tests (if applicable)
  • Check your code with any unit tests (Run devtools::check() locally)
  • Add neccessary documentation (if applicable)

Type of changes

What type of changes does your code introduce?
Put an x in the boxes that apply

  • Bugfix (non-breaking change which fixes an issue) (link the issue on the right)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • Code style update (formatting, renaming)
  • [X ] Documentation Update
  • Other (explain)

Further comments

If this is a relatively large or complex change, kick off the discussion by explaining why you chose the solution you did and what alternatives you considered, any questions you have, etc...

Consider linking any issues (#issue-number ) or adding @mentions to ensure specific people see it.

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@kathy-nevola kathy-nevola left a comment

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LGTM

+ The negative control contains an assay QC warning across all assays, excluding Olink's internal control assays
+ The negative control does not pass sample QC criteria (sample QC failure or warning) in all Explore HT blocks or all Explore 3072 panels

For each assay, the median NPX is calculated for all negative controls present in a project. For Explore 3072, overlapping assays are assessed separately, within their respective panels. The LOD for each assay is then calculated as the assay's median negative control NPX value plus 0.2 Standard Deviations.
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@kathy-nevola
median negative control NPX value plus 0.2 Standard Deviations. or

3 Standard Deviations or 0.2 whichever higher
?

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Good catch, fixed this

@kathy-nevola kathy-nevola merged commit 3faa92b into fix_lod May 30, 2024
15 of 16 checks passed
@kathy-nevola kathy-nevola deleted the lod_tutorial branch May 30, 2024 19:28
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3 participants