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nf-core / quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.
https://nf-co.re/quantms
MIT License
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Clarify/Unify exported scores #43

Closed jpfeuffer closed 7 months ago

jpfeuffer commented 2 years ago

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).

ypriverol commented 7 months ago

This issue has been open for a year and we are not working on it.