Bioconductor Dmpfinder

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methylset minfi dmpFinder betaHMM beta

updated 5 months ago by James W. MacDonald 68k • written 6 months ago by neyousha • 0

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minfi limma lmm lmfit dmpFinder

3.9 years ago kyleyxw • 0

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minfi methylation dmpfinder limma

updated 7.9 years ago by vulegom • 0 • written 8.6 years ago by mcall ▴ 20

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minfi dmpfinder dmp illuminahumanmethylationepicanno.ilmn10b.hg19 epic microarray

updated 8.8 years ago by James W. MacDonald 68k • written 8.8 years ago by Biologist ▴ 120

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minfi minfidata illumina methylation dmpfinder

updated 10.6 years ago by James W. MacDonald 68k • written 10.6 years ago by michael.zulyniak • 0

5 results • Page 1 of 1

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Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ktz • 0

Thank you for the quick reply. Rep 1 is lower than rep 2 in only one group (V_CD45), is this sufficient to affect the results even if I inc…

Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k

One clearly sees spread in this gene but it seems largely explained by "rep", so some sort of batch effect that you are already accounting …

Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ktz • 0

Thank you both for your reply and your time! Sorry I didn't include this earlier but here it is (for the gene of interest): structure(…

Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k

The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…

Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k

> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…

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Answer: Improving performance of edgeR and limma while adjusting for multiple confounder

Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin

Two EPIC Methylation Array Analysis Questions

How to get DMR for Infinium methylation EPIC v2

A: GEOquery Fails to Download Series Matrix File

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