Bioconductor ClassifyTestsF

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limma classifyTestsF

updated 10.0 years ago by Gordon Smyth 52k • written 18.2 years ago by Bandyopadhyay, Somnath Som ▴ 60

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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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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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