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Comment: ANOVA like approach of edgeR by Gordon Smyth 52k

To identify common upregulated or downregulated genes, you would need to test for media condition contrasts for each cell type separately, …

Comment: DESeq2 sizefactors counfounded with biological treatment by Anna • 0

Hi James, Apologies (re: posting in the wrong place). Thank you so much for your response, that was exactly the help I needed. Best, A…

Comment: ANOVA like approach of edgeR by Talip ▴ 10

I am comparing the expression patterns of different tissue cell lines (CellType) under five distinct media conditions (Status). Since the c…

Comment: Merge Replicates vs Mixed Model by gabriel.hoffman ▴ 160

It is almost always better to retain the full observed data, if the statistical software is able to model the repeated measures. This is a…

Comment: makeContrastsDream for Interaction by gabriel.hoffman ▴ 160

The simplest way to handle contrasts with an interaction term is to create a new variable. Lets consider a simpler case with variables `Se…

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Answer: ANOVA like approach of edgeR

Answer: Epic v2 Annotation CpG_maf source?

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