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Comment: Correct the batch effect in methylation analysis in R
by
Gordon Smyth
49k
> Is it okay to apply removeBatchEffect before a limma analysis(limma linear model)?
No, it is not ok to apply any batch correction before…
Comment: Correct the batch effect in methylation analysis in R
by
kyj2226
•
0
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
by
Gordon Smyth
49k
You should not apply batch correction functions like harman before a limma analysis. Instead, just add `batch` to the limma linear model.
…
Answer: Agilent Microarray Gene Oncology analysis gone wrong
by
Gordon Smyth
49k
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…
Comment: Normalised counts from RUVg in RUVSeq
by
Shaimaa Gamal
•
0
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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