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EdgeR
•
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9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 17 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
3
votes
3
replies
334
views
permutation test in edgeR
rna-seq
edgeR
updated 14 days ago by
Gordon Smyth
50k • written 27 days ago by
Netanel
• 0
1
vote
3
replies
348
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 20 days ago by
Gordon Smyth
50k • written 25 days ago by
Simran
• 0
4
votes
6
replies
427
views
FilterByExpr low counts with small sample size
edgeR
17 days ago • updated 12 days ago
Jonathan
▴ 10
3
votes
1
reply
176
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 16 days ago by
Gordon Smyth
50k • written 17 days ago by
Shaimaa Gamal
• 0
0
votes
3
replies
188
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 16 days ago by
Gordon Smyth
50k • written 16 days ago by
prity6459
• 0
0
votes
2
replies
133
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
16 days ago
prity6459
• 0
1
vote
3
replies
255
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 29 days ago by
James W. MacDonald
65k • written 29 days ago by
Shaimaa Gamal
• 0
1
vote
1
reply
176
views
Citation for edgeR user guide
edgeR
updated 11 days ago by
Gordon Smyth
50k • written 11 days ago by
k___
▴ 30
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 16 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
5
votes
6
replies
425
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 22 days ago by
ATpoint
★ 4.1k • written 26 days ago by
nhaus
▴ 30
0
votes
1
reply
92
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
z_bahari
• 0
1
vote
1
reply
310
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 2 days ago by
gene_bioconductor
▴ 10
13 results • Page
1 of 1
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Replies
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
Answer: Handling multiple differential expression comparisons
by
Michael Love
41k
It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
Comment: Too many significant genes when integrating gtex and tcga
by
ATpoint
★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Votes
Print Differentially Expressed Exons From Dexseq Results
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
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