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Question about PTM normalization #2

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BAREJAA opened this issue May 1, 2024 · 0 comments

BAREJAA commented May 1, 2024

Hi,

In your workflow, you correct PTM levels by "fitting a global linear model and returning residuals" (https://github.com/MoTrPAC/MotrpacRatTraining6moQCRep/blob/main/tools/ptm_protein_correction.R). I'm curious to know why you chose this approach versus fitting separate models for each PTM-protein matched pair?

Thank you!
Akshay

p.s. This is a wonderful project, and I really appreciate that you've made all this well-organized code available for the community.

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