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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 15 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 15 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
5
votes
6
replies
423
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 21 days ago by
ATpoint
★ 4.1k • written 24 days ago by
nhaus
▴ 30
4
votes
6
replies
417
views
FilterByExpr low counts with small sample size
edgeR
16 days ago • updated 11 days ago
Jonathan
▴ 10
1
vote
3
replies
345
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 19 days ago by
Gordon Smyth
50k • written 24 days ago by
Simran
• 0
0
votes
3
replies
182
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 15 days ago by
Gordon Smyth
50k • written 15 days ago by
prity6459
• 0
1
vote
3
replies
246
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 28 days ago by
James W. MacDonald
65k • written 28 days ago by
Shaimaa Gamal
• 0
3
votes
3
replies
327
views
permutation test in edgeR
rna-seq
edgeR
updated 13 days ago by
Gordon Smyth
50k • written 26 days ago by
Netanel
• 0
0
votes
2
replies
129
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
15 days ago
prity6459
• 0
1
vote
1
reply
170
views
Citation for edgeR user guide
edgeR
updated 10 days ago by
Gordon Smyth
50k • written 10 days ago by
k___
▴ 30
3
votes
1
reply
167
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 15 days ago by
Gordon Smyth
50k • written 16 days ago by
Shaimaa Gamal
• 0
0
votes
1
reply
81
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
z_bahari
• 0
0
votes
1
reply
168
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
updated 1 day ago by
Gordon Smyth
50k • written 1 day ago by
gene_bioconductor
▴ 10
13 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
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
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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