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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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how to get intensity values exclusively? #773

Open Adiya7 opened 1 year ago

Adiya7 commented 1 year ago

Hi Vadim,

We have an experiment that requires only intensity values without normalizition. I tried to run DIANN with the additional commands: --no-maxlfq --no-norm and the output tables were empty. [When in normal use (without these commands) a list of proteins was received as expected.] Why is this happening? what can we do to solve this problem?

TNX a lot!

michaelsteidel86 commented 1 year ago

Need More context.

I suspect you are interested in protein quan & are refering to matrix output tables - they actually show only MaxLFQ-based quantities. Have tried —no-norm only?

Best Michael

Adiya7 commented 1 year ago

Hi Michael, thanks for the quick response. Indeed, I hold an interest in the protein quantity. Unfortunately, the report.pg_matrix, which I find more user-friendly for manipulation, turned out to be blank. Is there a possible method to obtain this matrix containing unnormalized and non-LFQ values? Thanks.

michaelsteidel86 commented 1 year ago

If you want to have non-normalized non-MaxLFQ protein quantities 1) open report.tsv 2) apply filters according to the documentation (Q.Value < 0.01, Lib.Q.Value < 0.01 (in case of an MBR analysis) and GLobal.PG.Q.Value < 0.01) 3) 'PG.Quantity' is the non-normalised protein level quantity described in the original DIA-NN paper (non-MaxLFQ)