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Answer: Is it still possible to do batch correction for my data? by Gordon Smyth 53k

I agree with the comments from James MacDonald, but I will add that if you use the standard linear model correction for batch ``` design <-…

Answer: specifying refColumn in calcNormFactors() by Gordon Smyth 53k

Your question is about cross-validation rather than specifically about edgeR. A general principle of cross-validation is that you must norm…

Answer: Sex prediction in sesame for EPICV2 by Tim Peters ▴ 230

Hi Pooja, There is a tutorial for preprocessing EPICv2 via sesame here: https://clark-lab.github.io/EPICv2_tutorial/. There is no call t…

Comment: Convergence Issues and Model Selection DESeq2 by dani.guan.3 • 0

Thank you, I appreciate your time and help.

Comment: Convergence Issues and Model Selection DESeq2 by Michael Love 43k

> out of my 30,229 genes, 795 (2.6%) are better explained ... Not exactly. Frequentist statistics is not symmetric in this way. If it were…

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DiffBind dropping peaks in ATAC-seq data

A: decideTests() options in LIMMA

A: Removing cell cycle genes in large data set integration

Answer: Quick two questions on limpa

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