Bioconductor DGElist

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460

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DGEList edgeR

10 months ago prity6459 • 0

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837

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edgeR Bioconductor Dseq2 dgelist

updated 2.2 years ago by Gordon Smyth 52k • written 2.2 years ago by Fiona • 0

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1.1k

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factors edgeR setup DGELIst

updated 3.8 years ago by Gordon Smyth 52k • written 3.8 years ago by Alex • 0

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2.2k

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edger DGElist

updated 5.9 years ago by Gordon Smyth 52k • written 5.9 years ago by naser.sadri • 0

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2.0k

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dgelist edger RnaSeqGeneEdgeRQL

updated 6.6 years ago by Gordon Smyth 52k • written 6.6 years ago by Kevin • 0

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2.5k

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edgeR summarizedexperiment dgelist

6.9 years ago aljoscha.leusmann • 0

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1.1k

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tree bootstrap dgelist plotmds

7.0 years ago Larry K. • 0

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2.6k

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edger dgelist NA egsea

updated 7.0 years ago by Gordon Smyth 52k • written 7.0 years ago by belmore • 0

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4.2k

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edger DGEList org.hs.eg.db gene annotation

updated 3.4 years ago by IIart.hubII • 0 • written 7.3 years ago by svlachavas ▴ 840

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3.6k

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egder dgelist group rnaseq

updated 7.3 years ago by Aaron Lun ★ 28k • written 7.3 years ago by fawazfebin ▴ 60

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3.8k

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DGElist filter edgeR

updated 7.7 years ago by Gordon Smyth 52k • written 7.7 years ago by alakatos ▴ 130

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2.9k

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edger raw reads TMM normalised values DGEList differential gene expression

updated 8.6 years ago by Steve Lianoglou ★ 13k • written 8.6 years ago by benedict.ng ▴ 30

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7.3k

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edger subsetting dgelist

updated 8.6 years ago by Gordon Smyth 52k • written 8.6 years ago by mnaymik ▴ 10

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21k

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edgeR row.names DGEList

10.1 years ago ccheung • 0

14 results • Page 1 of 1

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Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840

Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …

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…

Votes

A: What is the "linear model" part used for in Limma?

Comment: Use of limma R package with targeted proteomics for DE analysis

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

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