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UCLouvain-CBIO / scp

Single cell proteomics data processing
https://uclouvain-cbio.github.io/scp/index.html
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refactor `divideByReference()` #34

Open cvanderaa opened 2 years ago

cvanderaa commented 2 years ago

I think we should consider several improvements:

  1. divideByReference() is a type of normalization (normalization by reference channel), therefore I think it should be made accessible from normalizeSCP(). This means we need to implement a new method in MsCoreUtils.
  2. Since it is a type of normalization, a new assay should be created instead of replacing the target assay.
  3. We could make it more generic, including subtraction as well (in case of normalization on log-transformed data).
cvanderaa commented 1 year ago

(point 1.): Strictly speaking, dividing all multiplexed samples within a run with a reference channel is batch correction rather than normalization (though many call it normalization anyway).