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Showing :
model.matrix
•
reset
3
votes
6
replies
268
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
8 weeks ago
mohammedtoufiq91
▴ 10
4
votes
6
replies
255
views
Question on creating right design matrix in edgeR
R
designmatrix
edgeR
limma
model.matrix
8 weeks ago
Abdul
▴ 10
1
vote
2
replies
173
views
Extracting specific comparisons after fitting model in EdgeR
edgeR
limma
design
RNASeq
model.matrix
9 weeks ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
157
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma
R
design
model.matrix
9 weeks ago
mohammedtoufiq91
▴ 10
1
vote
3
replies
270
views
Error: unexpected input in "mod <- model.matrix( ̃~"
model.matrix
12 weeks ago
p.m.craven
• 0
2
votes
2
replies
319
views
Help with constructing design matrix for edgeR/limma
limma
design.matrix
model.matrix
edgeR
8 months ago
adrianna_07
• 0
3
votes
6
replies
674
views
LogFC values in edgeR - w/wo intercept
design.matrix
logFC
intercept
edgeR
model.matrix
8 months ago
JK Kim
▴ 10
3
votes
4
replies
646
views
How to make design matrices or compare contrast in limma
designmatrices
differentialexpression
makeContrasts
limma
model.matrix
10 months ago
mohammedtoufiq91
▴ 10
0
votes
2
replies
800
views
RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq
model.matrix
edger
updated 2.6 years ago by
James W. MacDonald
62k • written 2.6 years ago by
lucap
• 0
2
votes
7
replies
988
views
Limma analysis with multiple variables
limma
model.matrix
de
design
rnaseq
updated 2.7 years ago by
Gordon Smyth
47k • written 2.7 years ago by
Will
• 0
0
votes
0
replies
383
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
3.2 years ago
ingerslev
• 0
1
vote
3
replies
441
views
Collapse Technical Replicates and Group-specific condition effects, individuals nested within groups
deseq2
RNAseq
model.matrix
collapseTechnicalReplicates
updated 3.2 years ago by
Michael Love
39k • written 3.2 years ago by
rbenel
▴ 20
3
votes
6
replies
1.8k
views
Understanding voom behavior when model matrix is used with/without intercept for a continuous variable
limma
voom
rnaseq
model.matrix
intercept
updated 3.2 years ago by
Gordon Smyth
47k • written 3.2 years ago by
atakanekiz
▴ 30
0
votes
0
replies
473
views
Blocking term for nested design in limma
limma
mixed-effects
model.matrix
3.4 years ago
Finn
• 0
1
vote
5
replies
533
views
DESEQ2 design matrix for double knockout interaction with condition
deseq2
model.matrix
design matrix
updated 3.7 years ago by
Michael Love
39k • written 3.7 years ago by
user9635643
• 0
3
votes
2
replies
507
views
model matrix design for DESeq2 for use with lfcShrink function
deseq2
model.matrix
updated 3.9 years ago by
Michael Love
39k • written 3.9 years ago by
toddknutson
• 0
4
votes
7
replies
1.9k
views
LIMMA time series spline model.matrix design setup
limma
design
model.matrix
time series
splines
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
tleona3
• 0
0
votes
4
replies
559
views
DESeq2 analysis design - different individuals for all samples
deseq2
rnaseq
model.matrix
experimental design
4.2 years ago
Maithê Barros
▴ 10
1
vote
9
replies
832
views
shRNA-Seq analysis using edgeR
shrnaseq
edger
experimental design
model.matrix
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
6
replies
765
views
Custom model matrix for multi factordesign
deseq2
LRT
geometric mean
estimatesizefactors
model.matrix
updated 4.4 years ago by
Michael Love
39k • written 4.4 years ago by
carol.brunel
• 0
7
votes
3
replies
3.7k
views
[limma] Define contrasts for model with covariates
limma
model.matrix
makecontrasts
updated 4.6 years ago by
Gordon Smyth
47k • written 4.6 years ago by
enricoferrero
▴ 650
4
votes
4
replies
1.1k
views
edgeR: How can I determine which factors significantly explain my DE genes?
edger
differential gene expression
model.matrix
design matrix
updated 4.7 years ago by
Gordon Smyth
47k • written 4.7 years ago by
Robert Gilmore
• 0
1
vote
2
replies
658
views
Study design in DESeq2
deseq2
Model matrix not full rank
model.matrix
study design
4.8 years ago
Krzysztof Kolmus
▴ 10
4
votes
4
replies
752
views
edgeR: Choice of reference group in nested model
edgeR
model.matrix
nested design
reference group
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
ri.lars
▴ 40
4
votes
2
replies
757
views
How does the function model.matrix (to define experimental design) really works ?
experimental design
model.matrix
edger
updated 4.9 years ago by
Ryan C. Thompson
7.8k • written 4.9 years ago by
Aurora
▴ 20
1
vote
7
replies
1.0k
views
model.matrix from GDS data
model.matrix
lmFit
eBayes
GEOquery
limma
5.0 years ago
darthratus
• 0
2
votes
4
replies
1.3k
views
Matrix not full rank - DESeq2
deseq2
model matrix not full rank
model.matrix
deseq
differential binding analysis
updated 5.1 years ago by
Simon Anders
★ 3.7k • written 5.1 years ago by
rbronste
▴ 60
9
votes
1
reply
2.7k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2
model.matrix
GLM
contrast
updated 5.1 years ago by
Michael Love
39k • written 5.1 years ago by
serpalma.v
▴ 60
1
vote
2
replies
804
views
Mixed conditions: Design and contrast matrix
limma
model.matrix
updated 5.2 years ago by
Ryan C. Thompson
7.8k • written 5.2 years ago by
Patrick
• 0
1
vote
3
replies
777
views
Matrix is not full rank with Multifactorial Experiment and Time course
deseq2
multiple factor design
model.matrix
time course
updated 5.3 years ago by
Michael Love
39k • written 5.3 years ago by
irving.jgalo23
• 0
2
votes
3
replies
1.1k
views
Differential expression of nomalised and log2 transformed data in limma
limma
lmfit
model.matrix
differential gene expression
5.4 years ago
stinehedensted
• 0
0
votes
1
reply
1.7k
views
RUVseq: How to implement to more complex time-course model?
ruvseq
deseq2
model.matrix
confounders
updated 5.5 years ago by
davide risso
▴ 920 • written 5.5 years ago by
heikki.sarin
▴ 10
5
votes
5
replies
1.7k
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
5.5 years ago
heikki.sarin
▴ 10
0
votes
0
replies
950
views
How construct a model for case-control time-course experiment in DEXseq?
dexseq
timecourse
model.matrix
model
5.5 years ago
heikki.sarin
▴ 10
0
votes
1
reply
1.2k
views
Proper dataset form and model for DEXeq analysis
dexseq
rna-seq
model.matrix
model
updated 5.5 years ago by
Michael Love
39k • written 5.5 years ago by
heikki.sarin
▴ 10
2
votes
3
replies
896
views
Issues about experiment design
limma
model.matrix
makecontrasts
5.9 years ago
TFony
▴ 10
0
votes
2
replies
941
views
Right use of model.matrix?
limma
agilent
microarray
lmfit
model.matrix
updated 6.2 years ago by
Gordon Smyth
47k • written 6.2 years ago by
Maximilian
▴ 10
0
votes
2
replies
1.2k
views
DESeq2 Model matrix design: Merging large RNAseq projects
deseq2
model.matrix
batch effect
rnaseq
6.4 years ago • updated 6.3 years ago
arom2
• 0
4
votes
3
replies
912
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 6.6 years ago by
Gavin Kelly
▴ 660 • written 6.6 years ago by
Peter
• 0
3
votes
10
replies
5.2k
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 6.6 years ago by
Gordon Smyth
47k • written 6.6 years ago by
manasishah86
▴ 30
2
votes
11
replies
1.2k
views
Adjusting for confounders along with paired testing using edgeR
edgeR
paired samples
confounders
model.matrix
updated 6.6 years ago by
Ryan C. Thompson
7.8k • written 6.6 years ago by
manasishah86
▴ 30
1
vote
3
replies
1.2k
views
limma overfitting model due to intercept and yet exclusion of intercept= uninterpretable results
limma
microarray
linear model
statistical modeling
model.matrix
6.7 years ago
christopher.clarskon15
▴ 20
1
vote
4
replies
1.2k
views
DESeq2 , model matrix with 4 factors, error: inv(): matrix appears to be singular
deseq2
multiple factor design
model.matrix
updated 6.7 years ago by
Michael Love
39k • written 6.7 years ago by
cdemel
• 0
0
votes
2
replies
1.3k
views
Random effects metagenomeSeq
model.matrix
updated 7.0 years ago by
noelle.noyes
▴ 30 • written 7.1 years ago by
PJ
• 0
2
votes
6
replies
2.3k
views
Understanding and creating various comparisons with model.matrix in limma regarding microarrays
limma
microarray
multifactorial design
duplicatecorrelation
model.matrix
7.1 years ago
Konstantinos Yeles
▴ 70
4
votes
4
replies
1.4k
views
Limma Nuisance Variable in an Interaction Model
limma
model.matrix
updated 7.2 years ago by
Ryan C. Thompson
7.8k • written 7.2 years ago by
andrew.j.skelton73
▴ 360
3
votes
4
replies
1.1k
views
Paired Experimental Design
limma
model.matrix
updated 7.3 years ago by
James W. MacDonald
62k • written 7.3 years ago by
andrew.j.skelton73
▴ 360
5
votes
3
replies
5.7k
views
Limma: Continuous variable model designs
limma
model.matrix
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
andrew.j.skelton73
▴ 360
0
votes
6
replies
1.5k
views
DESeq2 design model-mothers & offspring timepoint comparisons
model.matrix
multiple factor design
design and contrast matrix
deseq2
updated 7.5 years ago by
Michael Love
39k • written 7.5 years ago by
newmanss
• 0
3
votes
5
replies
1.4k
views
Complex Model Design with Bumphunter (Minfi)
minfi
bumphunter
model.matrix
linear model
7.6 years ago
andrew.j.skelton73
▴ 360
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 and heatmap for multiple comparisons
by
artem.vorobyev
• 0
this I already did. My question is how to visualize differentially expressed genes on the heatmap for all 3 groups (healty->lesion->treat…
Comment: athPkgBuilder data source :missing probesets
by
nicklesteele532
• 0
> >>> > >>> How to handle the one probeset to multiple locus mappings? I can > >think 3 > >>> possible solutions: > >>> 1. pick the "best" …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
> sum(width(gr_toexclude)) [1] 2713499861 I excluded everything which was not locus. If small rna locus is from 2000 to 4000 and next locu…
Comment: Why in Bioconductor community people rarely upvote questions?
by
Hervé Pagès
16k
BTW I fail to see how the lack of upvotes to a question would be discouraging as long as you get a good answer. OTOH I can see how failing …
Answer: DESeq2 and heatmap for multiple comparisons
by
swbarnes2
★ 1.2k
If you want to know what genes are different between lesion and treated, compare them to each other.
Votes
Comment: recount 3 protect read length metadata
Answer: Doubts about manipulation and annotation of microarray files deposited at GEO
C: Batch correction in DESeq2
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
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