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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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About standardization #550

Open lbwfff opened 2 years ago

lbwfff commented 2 years ago

Hi Vadim,

Since I don't have a powerful server, I often calculate a large amount of data in batches, and I am concerned about whether this will affect the normalization. So I want to ask, is it necessary to analyze the data at one time to get good standardization, or is it possible to calculate in batches?

Thanks, LeeLee

vdemichev commented 2 years ago

Hi LeeLee,

Yes, this will affect normalisation. On the other hand, there are batch effects in the data anyway, so processing different mass spec batches separately and applying batch correction afterwards is fine. To reduce computational batch effects, please pre-select fragment ions to be used to quantify peptides, see "Can I implement incremental data processing of large-scale experiments based on DIA-NN?" here https://github.com/vdemichev/DiaNN#frequently-asked-questions

Best, Vadim