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designmatrix
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408
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
4 months ago • updated 3 months ago
Tadeoye
▴ 20
0
votes
1
reply
433
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 9 months ago by
James W. MacDonald
68k • written 9 months ago by
Neha
• 0
0
votes
3
replies
738
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 11 months ago by
Gordon Smyth
52k • written 11 months ago by
prity6459
• 0
0
votes
1
reply
447
views
Limma design matrix only showing 3/4 treatments?
limma
designmatrix
updated 12 months ago by
Gordon Smyth
52k • written 12 months ago by
avery
• 0
3
votes
5
replies
1.4k
views
Design for DE analysis in tidybulk
DESeq2
designmatrix
edgeR
limma
tidybulk
updated 2.2 years ago by
Michael Love
43k • written 2.2 years ago by
aditya.m
▴ 10
4
votes
6
replies
1.6k
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
2.3 years ago
Abdul
▴ 20
2
votes
4
replies
1.8k
views
DESeq2/edgeR/limma help with most appropriate design matrix
DESeq2
limma
modelmatrix
edgeR
designmatrix
updated 3.4 years ago by
Gordon Smyth
52k • written 3.5 years ago by
rebecca.lea.johnston
• 0
0
votes
3
replies
1.5k
views
DESeq2 Design Matrix Two Conditions and Two Treatments
designmatrix
deseq2
DESeq2
updated 3.5 years ago by
swbarnes2
★ 1.4k • written 3.5 years ago by
OST
• 0
1
vote
2
replies
1.4k
views
multifactorial design matrix
designmatrix
RNA-seq
limma
updated 4.0 years ago by
Gordon Smyth
52k • written 4.0 years ago by
athief
▴ 20
1
vote
0
replies
885
views
Design Matrix for multiple variables in Edge R
designmatrix
DifferentialExpression
edgeR
RNAseq
4.1 years ago
nageshprabhu.k
▴ 10
2
votes
4
replies
1.3k
views
edgeR design matrix for multiple factors
MutlipleFactors
DesignMatrix
edgeR
4.2 years ago
Debayan
▴ 20
0
votes
2
replies
1.3k
views
Help creating a paired sample design matrix in edgeR
edgeR
pairedsamples
designmatrix
4.2 years ago
sfidemw
• 0
0
votes
2
replies
1.0k
views
DESEQ2: Error in checkFullRank(modelMatrix)
deseq2
miRNASeq
designmatrix
Batch
updated 5.0 years ago by
Michael Love
43k • written 5.0 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 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
Beginner
▴ 60
2
votes
6
replies
1.4k
views
Limma DesignMatrix, dropping terms
Limma
designMatrix
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
Keifa
▴ 10
2
votes
4
replies
1.6k
views
design matrix for complicated experimental design in limma
limma
microarray
designmatrix
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 years ago by
nashchem
• 0
16 results • Page
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Answer: DNAStringSet(x, start=, end=) loses quality information
by
stenlana035
• 0
Perhaps the hub genes are associated with other variables that have a negative correlation with the immune score rather than the immunologi…
Answer: Model performance for spline modelling of RNA-seq timecourses in edgeR
by
Gordon Smyth
52k
I don't understand your question, because there is no difference between limma or glmFit or glmQLFit in terms of spline modeling or the tes…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
• 0
Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0 ![enter image description here][1]…
Answer: DESeq2 - am I extracting results incorrectly?
by
James W. MacDonald
68k
If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…
Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
by
Luca
• 0
I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…
Votes
Limma outputs different results for same sample?
Answer: Improving performance of edgeR and limma while adjusting for multiple confounder
Comment: DESeq - help with pair wise comparisons
Answer: Is random access by row index possible for an indexed VCF file?
Answer: Is random access by row index possible for an indexed VCF file?
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