Bioconductor MA plot

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DiffBind MA plot normalization ChIP-seq

updated 4.6 years ago by Rory Stark ★ 5.2k • written 4.6 years ago by hasse.bossenbroek • 0

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diffbind ma plot

updated 8.0 years ago by Rory Stark ★ 5.2k • written 8.0 years ago by rbronste ▴ 60

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MA Plot

updated 9.9 years ago by James W. MacDonald 68k • written 9.9 years ago by pablo_calza • 0

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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…

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