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ChIPSeq profileplyr DiffBind

updated 2.3 years ago by doug.barrows ▴ 20 • written 2.4 years ago by zhuyi05 • 0

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profileplyr ATACSeq DiffBind ComplexHeatmap ChIPSeq

updated 12 months ago by Junsik • 0 • written 2.5 years ago by Rory Stark ★ 5.1k

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profileplyr

2.8 years ago alexandre.blais ▴ 50

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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, you should not 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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