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Designmatrix
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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 18 months ago by
James W. MacDonald
68k • written 18 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
626
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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Comment: Question about the filterByExpr function inputs in edgeR
by
Gordon Smyth
53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
JKim
• 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
James W. MacDonald
68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Comment: Question about the filterByExpr function inputs in edgeR
by
mohammedtoufiq91
▴ 10
@gordonsmyth Yes, Gender is more a nuisance factor in our experiment, and our primary interest is to compare groups. I will just use filter…
Comment: Joining different datasets and analyzing using the group-specific condition effe
by
jason.chai
• 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Votes
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
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
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