Bioconductor DEGraph

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RNASeqData DEGraph RNASeq edgeR DegNorm

written 7 months ago by Shaozhen • 0

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rnaseqGene edgeR DEGraph DifferentialExpression

updated 11 months ago by Gordon Smyth 52k • written 11 months ago by z_bahari • 0

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GO DEGraph GO DEGraph

14.0 years ago Dick Beyer ★ 1.4k

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Pathways Network SPIA DEGraph Pathways Network SPIA DEGraph

updated 14.0 years ago by January Weiner ▴ 370 • written 14.0 years ago by laurent jacob ▴ 100

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Comment: orgDB by shepherl 4.1k

You should look at the documentation on the help pages for those packages. It should be clear enough there. But to speed things along: `…

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…

Votes

Calculating TOM in blockwise WGCNA

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.

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