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Showing :
model.matrix
•
reset
3
votes
9
replies
1.7k
views
Question about filter by expression (filterByExpr) in edgeR
CPM
filterByExpr
edgeR
design
model.matrix
13 months ago • updated 12 months ago
mohammedtoufiq91
▴ 10
1
vote
1
reply
737
views
Batch effect: Is it correct to put ~0 preparing the model.matrix to remove batch effect?
edgeR
model.matrix
BatchEffect
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
greta
• 0
3
votes
6
replies
978
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
16 months ago
mohammedtoufiq91
▴ 10
4
votes
6
replies
1.2k
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
16 months ago
Abdul
▴ 20
1
vote
2
replies
742
views
Extracting specific comparisons after fitting model in EdgeR
edgeR
limma
design
RNASeq
model.matrix
16 months ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
777
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma
R
design
model.matrix
16 months ago
mohammedtoufiq91
▴ 10
1
vote
3
replies
1.2k
views
Error: unexpected input in "mod <- model.matrix( ̃~"
model.matrix
17 months ago
p.m.craven
• 0
2
votes
2
replies
836
views
Help with constructing design matrix for edgeR/limma
limma
design.matrix
model.matrix
edgeR
23 months ago
adrianna_07
• 0
5
votes
6
replies
1.8k
views
LogFC values in edgeR - w/wo intercept
design.matrix
logFC
intercept
edgeR
model.matrix
23 months ago
JK Kim
▴ 20
3
votes
4
replies
1.3k
views
How to make design matrices or compare contrast in limma
designmatrices
differentialexpression
makeContrasts
limma
model.matrix
2.0 years ago
mohammedtoufiq91
▴ 10
0
votes
2
replies
1.3k
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq
model.matrix
edger
updated 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
lucap
• 0
2
votes
7
replies
1.9k
views
Limma analysis with multiple variables
limma
model.matrix
de
design
rnaseq
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 years ago by
Will
• 0
0
votes
0
replies
674
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
4.4 years ago
ingerslev
• 0
1
vote
3
replies
882
views
Collapse Technical Replicates and Group-specific condition effects, individuals nested within groups
deseq2
RNAseq
model.matrix
collapseTechnicalReplicates
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
rbenel
▴ 40
3
votes
6
replies
3.1k
views
Understanding voom behavior when model matrix is used with/without intercept for a continuous variable
limma
voom
rnaseq
model.matrix
intercept
updated 4.4 years ago by
Gordon Smyth
50k • written 4.4 years ago by
atakanekiz
▴ 30
0
votes
0
replies
799
views
Blocking term for nested design in limma
limma
mixed-effects
model.matrix
4.6 years ago
Finn
• 0
1
vote
5
replies
932
views
DESEQ2 design matrix for double knockout interaction with condition
deseq2
model.matrix
design matrix
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
user9635643
• 0
3
votes
2
replies
856
views
model matrix design for DESeq2 for use with lfcShrink function
deseq2
model.matrix
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
toddknutson
• 0
4
votes
7
replies
3.1k
views
LIMMA time series spline model.matrix design setup
limma
design
model.matrix
time series
splines
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
tleona3
• 0
0
votes
4
replies
940
views
DESeq2 analysis design - different individuals for all samples
deseq2
rnaseq
model.matrix
experimental design
5.4 years ago
Maithê Barros
▴ 10
1
vote
9
replies
1.5k
views
shRNA-Seq analysis using edgeR
shrnaseq
edger
experimental design
model.matrix
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
6
replies
1.2k
views
Custom model matrix for multi factordesign
deseq2
LRT
geometric mean
estimatesizefactors
model.matrix
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
carol.brunel
• 0
9
votes
3
replies
5.0k
views
[limma] Define contrasts for model with covariates
limma
model.matrix
makecontrasts
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
enricoferrero
▴ 660
4
votes
4
replies
1.7k
views
edgeR: How can I determine which factors significantly explain my DE genes?
edger
differential gene expression
model.matrix
design matrix
updated 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
Robert Gilmore
• 0
1
vote
2
replies
1.1k
views
Study design in DESeq2
deseq2
Model matrix not full rank
model.matrix
study design
6.0 years ago
Krzysztof Kolmus
▴ 10
4
votes
4
replies
1.3k
views
edgeR: Choice of reference group in nested model
edgeR
model.matrix
nested design
reference group
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
ri.lars
▴ 40
4
votes
2
replies
1.1k
views
How does the function model.matrix (to define experimental design) really works ?
experimental design
model.matrix
edger
updated 6.1 years ago by
Ryan C. Thompson
★ 7.9k • written 6.1 years ago by
Aurora
▴ 20
1
vote
7
replies
1.6k
views
model.matrix from GDS data
model.matrix
lmFit
eBayes
GEOquery
limma
6.2 years ago
darthratus
• 0
2
votes
4
replies
1.8k
views
Matrix not full rank - DESeq2
deseq2
model matrix not full rank
model.matrix
deseq
differential binding analysis
updated 6.3 years ago by
Simon Anders
★ 3.7k • written 6.3 years ago by
rbronste
▴ 60
9
votes
1
reply
4.4k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2
model.matrix
GLM
contrast
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
serpalma.v
▴ 60
1
vote
2
replies
1.1k
views
Mixed conditions: Design and contrast matrix
limma
model.matrix
updated 6.4 years ago by
Ryan C. Thompson
★ 7.9k • written 6.4 years ago by
Patrick
• 0
1
vote
3
replies
1.1k
views
Matrix is not full rank with Multifactorial Experiment and Time course
deseq2
multiple factor design
model.matrix
time course
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
irving.jgalo23
• 0
2
votes
3
replies
1.7k
views
Differential expression of nomalised and log2 transformed data in limma
limma
lmfit
model.matrix
differential gene expression
6.6 years ago
stinehedensted
• 0
0
votes
1
reply
2.1k
views
RUVseq: How to implement to more complex time-course model?
ruvseq
deseq2
model.matrix
confounders
updated 6.7 years ago by
davide risso
▴ 950 • written 6.7 years ago by
heikki.sarin
▴ 10
5
votes
5
replies
2.3k
views
edgeR : How to test differential exon expression on case/control study across all time points when accounting for the within subject variability?
egdeR
multiple time points
model.matrix
differential exon usage
model
6.7 years ago
heikki.sarin
▴ 10
0
votes
0
replies
1.2k
views
How construct a model for case-control time-course experiment in DEXseq?
dexseq
timecourse
model.matrix
model
6.7 years ago
heikki.sarin
▴ 10
0
votes
1
reply
1.4k
views
Proper dataset form and model for DEXeq analysis
dexseq
rna-seq
model.matrix
model
updated 6.7 years ago by
Michael Love
41k • written 6.8 years ago by
heikki.sarin
▴ 10
2
votes
3
replies
1.2k
views
Issues about experiment design
limma
model.matrix
makecontrasts
7.1 years ago
TFony
▴ 10
0
votes
2
replies
1.3k
views
Right use of model.matrix?
limma
agilent
microarray
lmfit
model.matrix
updated 7.4 years ago by
Gordon Smyth
50k • written 7.5 years ago by
Maximilian
▴ 10
0
votes
2
replies
1.6k
views
DESeq2 Model matrix design: Merging large RNAseq projects
deseq2
model.matrix
batch effect
rnaseq
7.6 years ago • updated 7.5 years ago
arom2
• 0
4
votes
3
replies
1.3k
views
What is the correct contrast matrix if one treatment must be compared to both of the other two treatments, but separately?
edger
limma
model.matrix
contrast matrix
design matrix
updated 7.8 years ago by
Gavin Kelly
▴ 680 • written 7.8 years ago by
Peter
• 0
3
votes
10
replies
6.8k
views
Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : newsplit: out of vertex space in paired edgeR comparison
edger
paired samples
model.matrix
estimatedisp
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
manasishah86
▴ 30
2
votes
11
replies
1.7k
views
Adjusting for confounders along with paired testing using edgeR
edgeR
paired samples
confounders
model.matrix
updated 7.8 years ago by
Ryan C. Thompson
★ 7.9k • written 7.8 years ago by
manasishah86
▴ 30
1
vote
3
replies
1.5k
views
limma overfitting model due to intercept and yet exclusion of intercept= uninterpretable results
limma
microarray
linear model
statistical modeling
model.matrix
7.9 years ago
christopher.clarskon15
▴ 20
1
vote
4
replies
1.5k
views
DESeq2 , model matrix with 4 factors, error: inv(): matrix appears to be singular
deseq2
multiple factor design
model.matrix
updated 7.9 years ago by
Michael Love
41k • written 7.9 years ago by
cdemel
• 0
0
votes
2
replies
1.7k
views
Random effects metagenomeSeq
model.matrix
updated 8.2 years ago by
noelle.noyes
▴ 30 • written 8.3 years ago by
PJ
• 0
2
votes
6
replies
2.8k
views
Understanding and creating various comparisons with model.matrix in limma regarding microarrays
limma
microarray
multifactorial design
duplicatecorrelation
model.matrix
8.4 years ago • updated 8.3 years ago
Konstantinos Yeles
▴ 80
4
votes
4
replies
1.7k
views
Limma Nuisance Variable in an Interaction Model
limma
model.matrix
updated 8.4 years ago by
Ryan C. Thompson
★ 7.9k • written 8.4 years ago by
andrew.j.skelton73
▴ 370
3
votes
4
replies
1.4k
views
Paired Experimental Design
limma
model.matrix
updated 8.5 years ago by
James W. MacDonald
65k • written 8.5 years ago by
andrew.j.skelton73
▴ 370
5
votes
3
replies
6.9k
views
Limma: Continuous variable model designs
limma
model.matrix
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
andrew.j.skelton73
▴ 370
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Comment: DESeq2 - dispersion estimation when there is none
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WardDeb
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Thank you for the pointers, I'll revert back again to the method section of the paper. As for the negative relationship of the estimated di…
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Hello James, How to generate the db? By running the makeOrgPackageFromNCBI() command? I have tried doing that, first by just deleting the …
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