Bioconductor DifferentialRegulation

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DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment

updated 19 days ago by Michael Love 43k • written 24 days ago by Sahil • 0

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1.3k

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DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation

9 months ago sajadahmad41454 • 0

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695

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Proteomics DifferentialRegulation limma

18 months ago svlachavas ▴ 840

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1.1k

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edgeR RNASeq DifferentialRegulation

updated 22 months ago by Gordon Smyth 52k • written 22 months ago by bioinfoWanderer • 0

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1.8k

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DESeq2 Dese DifferentialRegulation differe

updated 8 months ago by ij283 • 0 • written 23 months ago by Bernardo ▴ 10

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771

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ALL The DifferentialRegulation PathNet

written 2.1 years ago by Mine • 0

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1.4k

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limma seed DifferentialRegulation

updated 2.1 years ago by Gordon Smyth 52k • written 2.1 years ago by TSauer • 0

7 results • Page 1 of 1

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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k

If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…

Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0

why aren't there any answers?

Comment: Too many significant genes when integrating gtex and tcga by Jane • 0

I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…

Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180

Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…

Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k

No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…

Votes

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

Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct

Answer: Group-specific condition effects with individuals nested: matrix is not full ra

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