Bioconductor Linear models

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deseq2 design matrix multi-confounders linear models rna-seq

updated 5.1 years ago by Michael Love 43k • written 5.1 years ago by mohamedrefaat.1.1992 • 0

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methylation ComBat Linear models batch correction AIC

updated 5.3 years ago by Kevin Blighe ★ 4.0k • written 5.3 years ago by lucasmiranda42 • 0

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Limma R Linear Models

updated 6.1 years ago by Aaron Lun ★ 28k • written 6.1 years ago by christiangriffioen • 0

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ballgown linear models

7.0 years ago Yong Li ▴ 50

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microarray SVA ComBat Linear models Residuals

7.7 years ago DataFanatic ▴ 10

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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(…

Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30

I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…

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…

Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0

Thank you so much for sharing the link.

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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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