Bioconductor Carpentries

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Carpentries Community Teaching Bioconductor

6 months ago Maria Doyle ▴ 100

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teaching Carpentries

2.4 years ago Maria Doyle ▴ 100

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teaching Carpentries

written 2.6 years ago by Laurent Gatto 1.6k

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

Underpowerment and notable noise/variability, that's the answer.

Comment: DESeq - help with pair wise comparisons by ATpoint ★ 4.8k

It's exactly this, no? https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#group-specific-condition-effect…

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

Sorry for the repetitive questions! I'm actually just trying to understand it better so that I can explain to the wet lab biologists in my …

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

> Would you advice against running deseq separately for each comparison? You're reducing power even more. Look, since you appear a bit "de…

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…

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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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