Currently, the main method in the application for downstream analysis is MSststas. However, Proteus, a limma-based package for TMT and LFQ can be also used in pquantr. Before the implementation in the package, the following task should be done:
[ ] Benchmark Proteus and MSstats for TMT and LFQ data. Explore the differences.
[ ] If Proteus offers better results, implement Proteus as an alternative downstream analysis package.
[ ] Release a new version of the tool with both packages.
Even if Proteus is not implemented after the benchmark. Would be great @Douerww to keep track of that benchmark for future decisions about the project and also for publication purpose.
Currently, the main method in the application for downstream analysis is MSststas. However, Proteus, a limma-based package for TMT and LFQ can be also used in pquantr. Before the implementation in the package, the following task should be done:
Even if Proteus is not implemented after the benchmark. Would be great @Douerww to keep track of that benchmark for future decisions about the project and also for publication purpose.