Bioconductor CompareCluster

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emapplot enrichplot clusterProfiler compareCluster

updated 3.9 years ago by Guido Hooiveld ★ 3.8k • written 3.9 years ago by rapmic • 0

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comparecluster chipseq

5.4 years ago Ashley • 0

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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 …

Comment: enrichGOgradient color change by James W. MacDonald 64k

You could look at my answer and extrapolate from there.

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Answer: enrichGOgradient color change

Answer: Filter genes by expression for voomLmFit

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