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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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DIA NN 1.19.1 problems #1203

Open haiyan-MS opened 3 weeks ago

haiyan-MS commented 3 weeks ago

When I used the 1.19.1 version, there is a contaminant option, when I choose it, the contaminants were not added to the search. Altrhough I saw you have a database for it. There is another more "serious" problem, I saw the report file, some of the protein groups has all LFQ value 0. How did it ever get there? In 1.18.1, there is empty cells for LFQ but now some are 0, some are empty. What is the difference?

vdemichev commented 3 weeks ago

Hi,

Contaminants will only appear if added also during predicted library generation.

some of the protein groups has all LFQ value 0

This is valid and means that's the best estimate DIA-NN can provide given the data. In most cases you might want to just filter those out.

Best, Vadim