Bioconductor DecideTests

Showing : decideTests • reset

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decideTests topTable limma

updated 20 months ago by Gordon Smyth 52k • written 20 months ago by Anna ▴ 20

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874

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edgeR voom decidetests DEG

updated 23 months ago by Gordon Smyth 52k • written 23 months ago by Ankita • 0

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1.6k

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limma eBayes decideTests topTable

updated 5.0 years ago by Gordon Smyth 52k • written 5.0 years ago by irene.roman • 0

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1.6k

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limma stageR decideTests

updated 6.1 years ago by Koen Van den Berge ▴ 180 • written 6.1 years ago by maltethodberg ▴ 180

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962

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limma decidetests

updated 6.4 years ago by Gordon Smyth 52k • written 6.4 years ago by Ryan C. Thompson ★ 7.9k

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1.8k

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limma anova decidetests

updated 6.4 years ago by Gordon Smyth 52k • written 6.4 years ago by mikhael.manurung ▴ 280

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limma decidetests

updated 7.4 years ago by Aaron Lun ★ 28k • written 7.4 years ago by jamie.gearing ▴ 60

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1.2k

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limma decidetests

updated 8.3 years ago by Gordon Smyth 52k • written 8.3 years ago by ahmed.asadik • 0

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limma decidetests

updated 8.4 years ago by Axel Klenk ★ 1.1k • written 8.4 years ago by bi_Scholar • 0

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limma decidetests methylation

updated 9.0 years ago by Sean Davis 21k • written 9.0 years ago by kraiczy ▴ 10

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rnaseq decideTests limma qvalue

9.7 years ago anver • 0

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limma B stats decideTests

updated 2.6 years ago by chm • 0 • written 9.9 years ago by Elsa • 0

12 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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