Bioconductor Interaction

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962

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DESeq2 interaction coefficient LinearModel RNASeq

updated 2.3 years ago by Michael Love 43k • written 2.3 years ago by Pedro Milanez-Almeida ▴ 10

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850

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interaction DESeq2

updated 2.6 years ago by swbarnes2 ★ 1.4k • written 2.6 years ago by Tait • 0

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4.6k

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DifferentialExpression contrasts interaction DESeq2

written 2.8 years ago by Nicole ▴ 10

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965

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DESeq2 interaction pairwise

3.5 years ago Lucas • 0

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8.0k

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LRT DESeq2 interaction

updated 3.9 years ago by Kevin Blighe ★ 4.0k • written 4.0 years ago by annamariabugaj ▴ 10

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1.4k

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limma interaction

4.5 years ago Sindre ▴ 110

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1.4k

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DESeq2 interaction differential expression

updated 4.6 years ago by Michael Love 43k • written 4.7 years ago by charles.foster ▴ 160

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1.1k

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mircomb mrna mirna degs interaction

4.7 years ago andreia ▴ 10

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1.3k

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deseq2 interaction model

updated 4.7 years ago by Michael Love 43k • written 4.7 years ago by aec ▴ 90

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1.1k

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graphite interaction

updated 4.9 years ago by gabriele.sales ▴ 100 • written 4.9 years ago by emisecherre • 0

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1.9k

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deseq2 interaction

updated 5.1 years ago by sebastian.lobentanzer ▴ 60 • written 5.1 years ago by ktrns • 0

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1.5k

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random effects interaction limma rna-seq

5.8 years ago flippy23 • 0

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920

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edger deseq2 interaction design matrix

updated 6.0 years ago by James W. MacDonald 68k • written 6.0 years ago by Assa Yeroslaviz ★ 1.5k

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1.2k

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DEXSeq interaction

6.1 years ago zhenzuo2 • 0

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1.0k

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edge differential gene expression timecourse interaction

6.6 years ago rubi ▴ 110

15 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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