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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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Too low number of IDs with NNs: reverting to linear classifer #1204

Open joycelyny opened 1 month ago

joycelyny commented 1 month ago

We have a dataset with two groups that have empty results files when opening the report.tsv, and we think it may be because the linear classifer was used. Is there a way to override this manually?

vdemichev commented 1 month ago

Hi,

How does the log look like?

Best, Vadim

joycelyny commented 1 month ago

image_123650291

vdemichev commented 1 month ago

Likely means nothing is detectable in that run. What can increase ID numbers is including common contaminants, but it will not really help much in identifying the proteins of interest in that run.

joycelyny commented 1 month ago

I see! Are there suggested modifications to make within the DIA-NN workflow to prevent this? I have multiple experiments that seem to have the same problem.

vdemichev commented 1 month ago

That's most likely the problem with runs, not with DIA-NN. But can try with --mass-acc-cal 100 (and a DIA-based empirical spectral library), this will solve the problem if calibration is the issue. XICs look OK, everything else seems OK?