Showing : shrinkage • reset
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DESeq differential expression results are too stringet. How to relax my criteria
shrinkage DifferentialExpression DESeq2
updated 19 months ago by ★ 4.7k • written 19 months ago by ▴ 10
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2
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running apeglm on a normal model and multiple coefficients
shrinkage apeglm
2.9 years ago • updated 2.8 years ago Frederik Ziebell ▴ 30
2
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8
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3.0k
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DESeq2 : log2FC discrepencies between results and lfcShrink
deseq2 shrinkage
updated 2.3 years ago by 43k • written 5.0 years ago by ▴ 20
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2
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DESeq2: qualitatively different results between deseq2 v1.14 and deseq2 v1.22 when run with shrinkage
deseq2 shrinkage
updated 6.1 years ago by 43k • written 6.2 years ago by • 0
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8
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DESeq2: betaPrior changes significance dramatically
deseq2 betaPrior shrinkage significance
6.8 years ago brynedal ▴ 40
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3
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1.6k
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disagreement between log2FoldChange and lfcMLE in DESeq2
deseq2 log2fc shrinkage
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 90
6 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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