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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
7 weeks ago
Tadeoye
▴ 20
0
votes
1
reply
378
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 7 months ago by
James W. MacDonald
67k • written 7 months ago by
Neha
• 0
0
votes
3
replies
653
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 9 months ago by
Gordon Smyth
52k • written 9 months ago by
prity6459
• 0
0
votes
1
reply
410
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 10 months ago by
Gordon Smyth
52k • written 10 months ago by
avery
• 0
3
votes
5
replies
1.3k
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
aditya.m
▴ 10
4
votes
6
replies
1.5k
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
2.2 years ago
Abdul
▴ 20
2
votes
4
replies
1.7k
views
DESeq2/edgeR/limma help with most appropriate design matrix
DESeq2
limma
modelmatrix
edgeR
designmatrix
updated 3.3 years ago by
Gordon Smyth
52k • written 3.3 years ago by
rebecca.lea.johnston
• 0
0
votes
3
replies
1.4k
views
DESeq2 Design Matrix Two Conditions and Two Treatments
designmatrix
deseq2
DESeq2
updated 3.3 years ago by
swbarnes2
★ 1.4k • written 3.3 years ago by
OST
• 0
1
vote
2
replies
1.4k
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multifactorial design matrix
designmatrix
RNA-seq
limma
updated 3.8 years ago by
Gordon Smyth
52k • written 3.9 years ago by
athief
▴ 20
1
vote
0
replies
852
views
Design Matrix for multiple variables in Edge R
designmatrix
DifferentialExpression
edgeR
RNAseq
4.0 years ago
nageshprabhu.k
▴ 10
2
votes
4
replies
1.2k
views
edgeR design matrix for multiple factors
MutlipleFactors
DesignMatrix
edgeR
4.0 years ago
Debayan
▴ 20
0
votes
2
replies
1.2k
views
Help creating a paired sample design matrix in edgeR
edgeR
pairedsamples
designmatrix
4.0 years ago
sfidemw
• 0
0
votes
2
replies
943
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 4.9 years ago by
Michael Love
43k • written 4.9 years ago by
anshulmbi
• 0
0
votes
2
replies
1.1k
views
How to create design matrix for differential analysis within the same cell-line samples?
edger
r
differentialanalysis
rnaseq
designmatrix
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
Beginner
▴ 60
2
votes
6
replies
1.4k
views
Limma DesignMatrix, dropping terms
Limma
designMatrix
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
Keifa
▴ 10
2
votes
4
replies
1.5k
views
design matrix for complicated experimental design in limma
limma
microarray
designmatrix
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
nashchem
• 0
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Comment: displaying the differential expression with deseq2 over 4X2 samples with the in
by
Martijn
• 0
thanks James, but if I do pairwise analyses per subject, I get the impression that I only get the intercepts per gene. Do you mean regardin…
Comment: plyranges: find exact GRanges match keeping metadata columns
by
alexis.weinreb
• 0
Thank you, this does clarify the available options.
Answer: displaying the differential expression with deseq2 over 4X2 samples with the in
by
James W. MacDonald
67k
If you have paired data you should block on subject, which is algebraically the same as fitting a model on the difference between treated a…
Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq?
by
jodan
• 0
Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…
Answer: Unused arguments error without used arguments in GSVA?
by
jodan
• 0
It looks like the ssgseaParam function might not be passing the correct parameters to GSVA::gsva(). The error suggests that minSize and max…
Votes
Answer: Find exact GRanges match keeping metadata columns
Answer: Find exact GRanges match keeping metadata columns
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
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