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MannLabs / directlfq

Fast and accurate label-free quantification for small and very large numbers of proteomes
https://doi.org/10.1101/2023.02.17.528962
Apache License 2.0
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Query/feature request: batch correction #32

Closed aliibarry closed 5 months ago

aliibarry commented 6 months ago

I'm working with the CLI and am hoping to build in a batch-correction step for large datasets. My initial thoughts would be to use deactivate_normalization TRUE on peptide intensities which has already been normalized + undergone a batch correction externally to directLFQ. Is there a better approach, and if not, is there a recommended batch correction approach?

Many thanks

ammarcsj commented 6 months ago

Hi, yes your approach sounds good! I would do it like this, in case anything comes up, feel free to write again.