Bioconductor DGEList

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371

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DGEList edgeR

7 months ago prity6459 • 0

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778

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edgeR Bioconductor Dseq2 dgelist

updated 23 months ago by Gordon Smyth 51k • written 23 months ago by Fiona • 0

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1.0k

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factors edgeR setup DGELIst

updated 3.5 years ago by Gordon Smyth 51k • written 3.5 years ago by Alex • 0

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2.1k

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edger DGElist

updated 5.6 years ago by Gordon Smyth 51k • written 5.6 years ago by naser.sadri • 0

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1.9k

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dgelist edger RnaSeqGeneEdgeRQL

updated 6.3 years ago by Gordon Smyth 51k • written 6.3 years ago by Kevin • 0

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2.4k

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edgeR summarizedexperiment dgelist

6.6 years ago aljoscha.leusmann • 0

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1.1k

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tree bootstrap dgelist plotmds

6.7 years ago Larry K. • 0

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2.5k

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edger dgelist NA egsea

updated 6.7 years ago by Gordon Smyth 51k • written 6.7 years ago by belmore • 0

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4.0k

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edger DGEList org.hs.eg.db gene annotation

updated 3.2 years ago by IIart.hubII • 0 • written 7.0 years ago by svlachavas ▴ 830

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3.4k

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egder dgelist group rnaseq

updated 7.0 years ago by Aaron Lun ★ 28k • written 7.1 years ago by fawazfebin ▴ 60

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3.6k

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DGElist filter edgeR

updated 7.4 years ago by Gordon Smyth 51k • written 7.4 years ago by alakatos ▴ 130

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2.8k

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edger raw reads TMM normalised values DGEList differential gene expression

updated 8.3 years ago by Steve Lianoglou ★ 13k • written 8.3 years ago by benedict.ng ▴ 30

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7.1k

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edger subsetting dgelist

updated 8.3 years ago by Gordon Smyth 51k • written 8.3 years ago by mnaymik ▴ 10

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21k

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edgeR row.names DGEList

9.8 years ago ccheung • 0

14 results • Page 1 of 1

Recent ...

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Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by rcreed • 0

The updated version worked well on my data. Thank you!

Votes

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

A: Error in DESeqDataSet : some values in assay are not integers

Awards • All

Scholar to Haibo Liu ▴ 20