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Add linear model-based normalization functions #78

Merged
merged 7 commits into from
Dec 22, 2023
Merged

Add linear model-based normalization functions #78

merged 7 commits into from
Dec 22, 2023

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jorainer
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This PR adds functions that allow to perform a linear-model based normalization, which includes:

  • adjustment for injection index dependent signal drifts in LC-MS data
  • adjustment for batch effects

The functions perform row-wise adjustments, thus, a linear model if fitted for each "feature" separately, and the data will be adjusted (per feature) for this. Also, estimation of the bias can be performed on a subset of samples (e.g. QC samples) and applied in a second step to the full data set.

These functions are core/basic functions, more user convenient functions that base on these might be implemented elsewhere.

R/normalization.R Outdated Show resolved Hide resolved
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@philouail philouail left a comment

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All good to me, I put a few comments. Very excited to try it out ! The code is also super clear in my opinion.

@jorainer jorainer merged commit 9de8e4c into main Dec 22, 2023
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2 participants