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refactor divideByReference() #34

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cvanderaa opened this issue May 12, 2022 · 1 comment
Open

refactor divideByReference() #34

cvanderaa opened this issue May 12, 2022 · 1 comment

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@cvanderaa
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cvanderaa commented May 12, 2022

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
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(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).

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