Showing : model.matrix • reset
3
votes
6
replies
268
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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
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Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
8 weeks ago Abdul ▴ 10
1
vote
2
replies
173
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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 62k • written 2.6 years ago by • 0
2
votes
7
replies
988
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 2.7 years ago by 47k • written 2.7 years ago by • 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 39k • written 3.2 years ago by ▴ 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 47k • written 3.2 years ago by ▴ 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 39k • written 3.7 years ago by • 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 39k • written 3.9 years ago by • 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 ★ 28k • written 4.0 years ago by • 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 ★ 28k • written 4.2 years ago by ★ 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 39k • written 4.4 years ago by • 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 47k • written 4.6 years ago by ▴ 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 47k • written 4.7 years ago by • 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 ★ 28k • written 4.8 years ago by ▴ 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 7.8k • written 4.9 years ago by ▴ 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 ★ 3.7k • written 5.1 years ago by ▴ 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 39k • written 5.1 years ago by ▴ 60
1
vote
2
replies
804
views
Mixed conditions: Design and contrast matrix
limma model.matrix
updated 5.2 years ago by 7.8k • written 5.2 years ago by • 0
1
vote
3
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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 39k • written 5.3 years ago by • 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
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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 ▴ 920 • written 5.5 years ago by ▴ 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 39k • written 5.5 years ago by ▴ 10
2
votes
3
replies
896
views
Issues about experiment design
limma model.matrix makecontrasts
5.9 years ago TFony ▴ 10
0
votes
2
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941
views
Right use of model.matrix?
limma agilent microarray lmfit model.matrix
updated 6.2 years ago by 47k • written 6.2 years ago by ▴ 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 ▴ 660 • written 6.6 years ago by • 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 47k • written 6.6 years ago by ▴ 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 7.8k • written 6.6 years ago by ▴ 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 39k • written 6.7 years ago by • 0
0
votes
2
replies
1.3k
views
Random effects metagenomeSeq
model.matrix
updated 7.0 years ago by ▴ 30 • written 7.1 years ago by • 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 7.8k • written 7.2 years ago by ▴ 360
3
votes
4
replies
1.1k
views
Paired Experimental Design
limma model.matrix
updated 7.3 years ago by 62k • written 7.3 years ago by ▴ 360
5
votes
3
replies
5.7k
views
Limma: Continuous variable model designs
limma model.matrix
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 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 39k • written 7.5 years ago by • 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
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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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