Bioconductor DmpFinder

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642

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methylset minfi dmpFinder betaHMM beta

updated 4 months ago by James W. MacDonald 68k • written 4 months ago by neyousha • 0

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990

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minfi limma lmm lmfit dmpFinder

3.8 years ago kyleyxw • 0

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3.6k

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minfi methylation dmpfinder limma

updated 7.8 years ago by vulegom • 0 • written 8.5 years ago by mcall ▴ 20

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3.3k

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minfi dmpfinder dmp illuminahumanmethylationepicanno.ilmn10b.hg19 epic microarray

updated 8.7 years ago by James W. MacDonald 68k • written 8.7 years ago by Biologist ▴ 120

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2.2k

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minfi minfidata illumina methylation dmpfinder

updated 10.5 years ago by James W. MacDonald 68k • written 10.5 years ago by michael.zulyniak • 0

5 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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