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designMatrix
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0
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2
replies
780
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
13 months ago
Tadeoye
▴ 20
0
votes
1
reply
609
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 19 months ago by
James W. MacDonald
68k • written 19 months ago by
Neha
• 0
0
votes
3
replies
1.1k
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
prity6459
• 0
0
votes
1
reply
627
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
avery
• 0
3
votes
5
replies
1.8k
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
aditya.m
▴ 10
4
votes
6
replies
1.9k
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
3.1 years ago
Abdul
▴ 20
2
votes
4
replies
2.1k
views
DESeq2/edgeR/limma help with most appropriate design matrix
DESeq2
limma
modelmatrix
edgeR
designmatrix
updated 4.2 years ago by
Gordon Smyth
53k • written 4.3 years ago by
rebecca.lea.johnston
• 0
0
votes
3
replies
1.7k
views
DESeq2 Design Matrix Two Conditions and Two Treatments
designmatrix
deseq2
DESeq2
updated 4.2 years ago by
swbarnes2
★ 1.4k • written 4.2 years ago by
OST
• 0
1
vote
2
replies
1.7k
views
multifactorial design matrix
designmatrix
RNA-seq
limma
updated 4.8 years ago by
Gordon Smyth
53k • written 4.8 years ago by
athief
▴ 20
1
vote
0
replies
1.0k
views
Design Matrix for multiple variables in Edge R
designmatrix
DifferentialExpression
edgeR
RNAseq
4.9 years ago
nageshprabhu.k
▴ 10
2
votes
4
replies
1.5k
views
edgeR design matrix for multiple factors
MutlipleFactors
DesignMatrix
edgeR
4.9 years ago
Debayan
▴ 20
0
votes
2
replies
1.6k
views
Help creating a paired sample design matrix in edgeR
edgeR
pairedsamples
designmatrix
4.9 years ago
sfidemw
• 0
0
votes
2
replies
1.2k
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 5.8 years ago by
Michael Love
43k • written 5.8 years ago by
anshulmbi
• 0
0
votes
2
replies
1.4k
views
How to create design matrix for differential analysis within the same cell-line samples?
edger
r
differentialanalysis
rnaseq
designmatrix
updated 6.7 years ago by
Aaron Lun
★ 29k • written 6.7 years ago by
Beginner
▴ 60
2
votes
6
replies
1.7k
views
Limma DesignMatrix, dropping terms
Limma
designMatrix
updated 7.5 years ago by
Aaron Lun
★ 29k • written 7.5 years ago by
Keifa
▴ 10
2
votes
4
replies
1.9k
views
design matrix for complicated experimental design in limma
limma
microarray
designmatrix
updated 9.5 years ago by
Aaron Lun
★ 29k • written 9.5 years ago by
nashchem
• 0
16 results • Page
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Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR
by
mohammedtoufiq91
▴ 10
@gordonsmyth Noted, thank you very much.
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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