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9
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Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 8 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq
edgeR
RNASeq
edgeR
updated 24 days ago by
Gordon Smyth
50k • written 11.5 years ago by
Maria Keays
▴ 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 7 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR
edgeR
updated 27 days ago by
Gordon Smyth
50k • written 12.4 years ago by
Bogdan
▴ 670
5
votes
6
replies
400
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 13 days ago by
ATpoint
★ 4.0k • written 17 days ago by
nhaus
▴ 30
0
votes
4
replies
395
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
25 days ago • updated 24 days ago
Lucy
▴ 60
4
votes
6
replies
349
views
FilterByExpr low counts with small sample size
edgeR
9 days ago • updated 4 days ago
Jonathan
▴ 10
3
votes
5
replies
340
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 27 days ago by
Gordon Smyth
50k • written 29 days ago by
Fabian
• 0
1
vote
3
replies
327
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 11 days ago by
Gordon Smyth
50k • written 16 days ago by
Simran
• 0
0
votes
6
replies
316
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 28 days ago by
Gordon Smyth
50k • written 29 days ago by
Faisal
• 0
3
votes
3
replies
294
views
permutation test in edgeR
rna-seq
edgeR
updated 5 days ago by
Gordon Smyth
50k • written 18 days ago by
Netanel
• 0
1
vote
3
replies
231
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 21 days ago by
James W. MacDonald
65k • written 21 days ago by
Shaimaa Gamal
• 0
0
votes
2
replies
148
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
23 days ago
Marianna
▴ 20
0
votes
3
replies
133
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 7 days ago by
Gordon Smyth
50k • written 8 days ago by
prity6459
• 0
3
votes
1
reply
123
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 7 days ago by
Gordon Smyth
50k • written 8 days ago by
Shaimaa Gamal
• 0
1
vote
1
reply
94
views
Citation for edgeR user guide
edgeR
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
k___
▴ 30
0
votes
2
replies
92
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
7 days ago
prity6459
• 0
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Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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