Improvements in the pipeline

bigbio / quantms

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

https://quantms.org

MIT License

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Improvements in the pipeline #183

Closed ypriverol closed 7 months ago

ypriverol commented 2 years ago

Description of feature

In the PR #182 (see unresolved review comments) we found minor issues related with MSstats:

@qinchunyuan

[x] MSstats TMT weird code and import of MSstats. Plus remove the TODO for user contrasts. This should be possible already (double-check)
[x] Changelog and docu for DIA-NN rework
[x] double-check usage of empirical vs insilico library in DIA-NN module descriptions

daichengxin commented 2 years ago

Hi @ypriverol Can't I use the plot functions of MSstats in the MSstatsTMT script? even if they are inside the same container.

jpfeuffer commented 2 years ago

Are they? Is MSstats a dependency of MSstatsTMT? Does that work with conda as well? Please comment that part then.

daichengxin commented 2 years ago

Yes. MSstats is a dependency of MSstatsTMT https://www.bioconductor.org/packages/release/bioc/html/MSstatsTMT.html

daichengxin commented 2 years ago

MSstatsTMT used MSstats. https://rdrr.io/bioc/MSstatsTMT/src/R/proteinSummarization.functions.R

daichengxin commented 2 years ago

Now MSstats has not been imported, the source code of drawing is used directly. https://github.com/bigbio/quantms/pull/184/files#diff-c2f8ca314376fc9925b6c61cf03fdedffed5e5e66c01bd3f35b387387b98613a