How to get the pr.matrix.tsv from the main out by the user?

[xiaoxHuang]

Hi Vadim

Thanks for your work!

I used diann-1.8.1 in linux. I want to reproduce the pr.matrix.tsv from the main out. As you mentioned here: using global q-values for protein groups and both global and run-specific q-values for precursors

But there are Q.value, PG.Q.value, Global.Q.value, Global.PG.Q.value, Lib.Q.value, Lib.PG.Q.value in the main out. I want to know which one or some values are used as filters to get the pr.matrix? In the cmd line, I tried both --qvalue 0.01 --matrix-qvalue 0.01 and --qvalue 0.03 --matrix-qvalue 0.03. Then got the pr.matrix by Python to compare the results with those saved by DIANN. I can not reproduce the results sometimes.

You also mentioned that All the 'matrices' can be reproduced from the main .parquet report, if generated with precursor FDR set to 5%, using R or Python.

So, I wonder if the 'qvalue 0.05' is a must for user to reproduce by R or Python?

Thanks!

Best wishes