Bioconductor Syntenet

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syntenet Bacteria synteny

6 weeks ago kluongni • 0

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syntenet synteny Network

written 12 months ago by Alexandros • 0

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220

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syntenet microsynteny blocks synteny

4 months ago Alexandros • 0

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398

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Network syntenet Clustering coefficient

5 months ago Alexandros • 0

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syntenet

updated 10 months ago by Fabricio Almeida-Silva ▴ 40 • written 11 months ago by lwanderson8c • 0

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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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Answer: Correct the batch effect in methylation analysis in R

Answer: enrichGOgradient color change

Answer: Filter genes by expression for voomLmFit

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