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Clarify/Unify exported scores #43

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jpfeuffer opened this issue May 13, 2022 · 1 comment
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Clarify/Unify exported scores #43

jpfeuffer opened this issue May 13, 2022 · 1 comment
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enhancement Improvement for existing functionality

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@jpfeuffer
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Description of feature

In the documentation we should explain when which score will be exported.
And maybe unify the scores in the sense that we should always perform an FDR calculation in PLFQ even if the cutoff is set to 1.0. (Currently calculation is omitted and actually 1.0 is fixed since max_psm_fdr does not seem to be passed to PLFQ).
This can be a bit confusing since then you might have some q-values from the per-file FDR calculation in there. Maybe we should also call the scores different then (e.g. per-file q-value, experiment-wide q-value).
@jpfeuffer jpfeuffer added the enhancement Improvement for existing functionality label May 13, 2022
ypriverol added a commit that referenced this issue Aug 4, 2022
@ypriverol
Merge pull request #43 from ypriverol/dev
8056cf5 
improvements conda
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This issue has been open for a year and we are not working on it.

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enhancement Improvement for existing functionality
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