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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 14 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 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 13 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
5
votes
6
replies
416
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 20 days ago by
ATpoint
★ 4.1k • written 23 days ago by
nhaus
▴ 30
4
votes
6
replies
406
views
FilterByExpr low counts with small sample size
edgeR
15 days ago • updated 10 days ago
Jonathan
▴ 10
3
votes
3
replies
325
views
permutation test in edgeR
rna-seq
edgeR
updated 12 days ago by
Gordon Smyth
50k • written 25 days ago by
Netanel
• 0
3
votes
1
reply
163
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 13 days ago by
Gordon Smyth
50k • written 15 days ago by
Shaimaa Gamal
• 0
1
vote
3
replies
242
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 27 days ago by
James W. MacDonald
65k • written 27 days ago by
Shaimaa Gamal
• 0
1
vote
1
reply
162
views
Citation for edgeR user guide
edgeR
updated 9 days ago by
Gordon Smyth
50k • written 9 days ago by
k___
▴ 30
1
vote
3
replies
343
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 17 days ago by
Gordon Smyth
50k • written 23 days ago by
Simran
• 0
0
votes
3
replies
178
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
prity6459
• 0
0
votes
1
reply
138
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 4 hours ago by
Gordon Smyth
50k • written 12 hours ago by
gene_bioconductor
▴ 10
0
votes
1
reply
46
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 9 hours ago by
Gordon Smyth
50k • written 13 hours ago by
z_bahari
• 0
0
votes
2
replies
125
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
13 days ago
prity6459
• 0
0
votes
2
replies
159
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
29 days ago
Marianna
▴ 20
14 results • Page
1 of 1
Recent ...
Replies
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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