how to calculate pr_matrix.tsv

[hxxhust163]

Hi

Thanks for your work in DiaNN. I used Diann1.8.1 in linux system and have a few questions about '--qvalue' and '--matrix-qvalue' . With the same DIA data, spectral library and other params, I tested the combination of different 'qvalue' and 'matrix-qvalue'.

Following is the params and results. 20.9M is the size of the main out, while 529.1k is the size of pr_matrix.tsv.

My questions are:

Q1. when qvalue=0.01 and matrix-qvalue=0.01, by filtering 'Lib.PG.Q.Value'<=0.01 in main out and convert it into wide format, I can got a tsv containing 3891 precursors, which is the same as the pr_matrix.tsv reported by DiaNN. So, I think Diann also use this way to convert the main out into pr_matrix. Is it right?

Q2. when qvalue=1 and matrix-qvalue=0.01, by filtering 'Lib.PG.Q.Value'<=0.01 in main out and convert it into wide format, I can got a tsv containing 7559 precursors, which is larger then 5352 reported in pr_matrix.tsv. So, I wonder how is the 'pr_matrix' calculated? This situation also applies to qvalue=1, matrix-qvalue=1 and qvalue=1, matrix-qvalue=0.05, and you can see that the precursors are both 7218, which seems strange.

Q3. For qvalue=1, matrix-qvalue=0.01, let the main out called 'M1' and called the main out 'M2' in qvalue=0.01, matrix-qvalue=0.01. How can I got 'M2' from 'M1', as the qvalue=1 makes 'M1' a complete result. I tried by filtering 'Q.Value'<=0.01 in 'M1' and got a tsv containing 12948 rows, which is larger than 10075 in 'M2'. So, how to explain this?

I want to get a complete main out and calculate different FDR by my own based on the main out by running DiaNN only once. That is why I do the above comparison.

The results above make me confused. Maybe there is something wrong in my setting? I am writing to ask for help. Thanks very much!

Best wishes Xiaoxiang