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Answer: Selection of correct coefficients or contrasts in DESeq2 by James W. MacDonald 67k

Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…

Comment: How to generate circular cnetplot and color nodes and edges in the same plot ? by Blandine • 0

Thank you so much ! It's working !

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by James W. MacDonald 67k

Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…

Comment: Recount3 data correspond to TCGA data by Leonardo Collado Torres ★ 1.1k

Thanks @fep29! ^^

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0

I am in a similar situation. So, I have a matrix of beta values with row names as probe ids (which are annotated to hg38 as it is from harm…

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Comment: Recount3 data correspond to TCGA data

Answer: EdgeR Biological CVs

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