Bioconductor Offset

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edgeR limma offset

updated 5.6 years ago by Gordon Smyth 49k • written 5.6 years ago by catpaw.tw • 0

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edgeR EDASeq offset

updated 5.9 years ago by Aaron Lun ★ 28k • written 5.9 years ago by alakatos ▴ 130

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3

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3.6k

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limma agilent offset background correction microarray

updated 7.8 years ago by James W. MacDonald 64k • written 7.8 years ago by Konstantinos Yeles ▴ 80

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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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