Bioconductor DGEList

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edgeR row.names DGEList

9.2 years ago ccheung • 0

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edger subsetting dgelist

updated 7.8 years ago by Gordon Smyth 50k • written 7.8 years ago by mnaymik ▴ 10

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DGElist filter edgeR

updated 6.8 years ago by Gordon Smyth 50k • written 6.8 years ago by alakatos ▴ 130

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edgeR Bioconductor Dseq2 dgelist

updated 16 months ago by Gordon Smyth 50k • written 16 months ago by Fiona • 0

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edgeR summarizedexperiment dgelist

6.0 years ago aljoscha.leusmann • 0

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egder dgelist group rnaseq

updated 6.5 years ago by Aaron Lun ★ 28k • written 6.5 years ago by fawazfebin ▴ 60

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edger dgelist NA egsea

updated 6.2 years ago by Gordon Smyth 50k • written 6.2 years ago by belmore • 0

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edger DGEList org.hs.eg.db gene annotation

updated 2.6 years ago by IIart.hubII • 0 • written 6.4 years ago by svlachavas ▴ 830

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edger raw reads TMM normalised values DGEList differential gene expression

updated 7.7 years ago by Steve Lianoglou ★ 13k • written 7.7 years ago by benedict.ng ▴ 20

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dgelist edger RnaSeqGeneEdgeRQL

updated 5.7 years ago by Gordon Smyth 50k • written 5.7 years ago by Kevin • 0

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edger DGElist

updated 5.1 years ago by Gordon Smyth 50k • written 5.1 years ago by naser.sadri • 0

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factors edgeR setup DGELIst

updated 2.9 years ago by Gordon Smyth 50k • written 2.9 years ago by Alex • 0

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DGEList edgeR

6 days ago prity6459 • 0

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916

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tree bootstrap dgelist plotmds

6.1 years ago Larry K. • 0

14 results • Page 1 of 1

Recent ...

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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…

Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k

You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…

Votes

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0