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Comment: Correct the batch effect in methylation analysis in R
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kyj2226
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Thank you for your response Gordon :)
I've already run the code below, just add batch to the limma linear model
design <- model.matri…
Answer: Correct the batch effect in methylation analysis in R
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You should not apply batch correction functions like harman before a limma analysis. Instead, just add `batch` to the limma linear model.
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Your use of `coef=1` is incorrect, for reasons explained in the limma User's Guide. If you had simply left `coef` at the default, then thin…
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Hello
I was wondering if I should use ruv-corrected counts and ruv lib sizes to create a DGE object that can be used later for DE analysis …
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You could look at my answer and extrapolate from there.
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