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Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by Harry • 0
It's interesting to see how the normalization factors are all 1, yet the MA plot reflects changes, indicating that the normalization proces…
Comment: European Bioconductor Conference 2023 planning by Andrew • 0
Great information! This is a great opportunity for the computational biology community to connect and grow. @[Chill Guy Clicker][1] [1…
Comment: orgDB by Fatima • 0
how to do that?
Answer: Is it possible to model DNA methylation as a dose response in edgeR? by Gordon Smyth 52k
edgeR works with any linear model, so handles any combination of factors and covariates. If you include dose as a covariate in the linear m…
Comment: DepMap data mismatch by Laurent Gatto 1.6k
It might be due to different versions. The repacked/cleaned data in the `depmap` R/Bioconductor package is old, but the latest files can al…
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A: What is the "linear model" part used for in Limma?
Comment: Use of limma R package with targeted proteomics for DE analysis
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
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