bigbio/quantms

Benchmark skip pre-analysis vs full preanalysis.

ypriverol opened this issue · 2 comments

ypriverol commented

In a recent PR #335, we introduced the possibility to skip the pre-analysis step. Would be great to have some plots and results about how skipping pre-analysis will affect the final results. @daichengxin maybe reanalyzing one of the benchmark datasets for DIA without the pre-analysis step would be a good idea and share the results in here.

daichengxin commented

PXD026600 are used to benchmark. Each concentration has three technical replicates. Three strategies of library generation: 1. all files 2. select a file in each technical replicates group (total 16 file). 3. random sampling 16 files. Performance is indeed degraded, compared to the full library.

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ypriverol commented

Results are almost identical.