Showing : model.matrix • reset
2
votes
11
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1.7k
views
Adjusting for confounders along with paired testing using edgeR
edgeR paired samples confounders model.matrix
updated 7.8 years ago by ★ 7.9k • written 7.8 years ago by ▴ 30
3
votes
10
replies
6.9k
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 50k • written 7.8 years ago by ▴ 30
3
votes
9
replies
1.8k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
13 months ago mohammedtoufiq91 ▴ 10
1
vote
9
replies
1.5k
views
shRNA-Seq analysis using edgeR
shrnaseq edger experimental design model.matrix
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ★ 1.5k
4
votes
7
replies
3.2k
views
LIMMA time series spline model.matrix design setup
limma design model.matrix time series splines
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
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
7
replies
2.0k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 3.9 years ago by 50k • written 3.9 years ago by • 0
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 41k • written 5.6 years ago by • 0
0
votes
6
replies
1.8k
views
DESeq2 design model-mothers & offspring timepoint comparisons
model.matrix multiple factor design design and contrast matrix deseq2
updated 8.7 years ago by 41k • written 8.7 years ago by • 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 Konstantinos Yeles ▴ 80
3
votes
6
replies
995
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
16 months ago mohammedtoufiq91 ▴ 10
3
votes
6
replies
2.1k
views
Complex Model Design with Bumphunter (Minfi)
minfi bumphunter model.matrix linear model
updated 14 months ago by • 0 • written 8.8 years ago by ▴ 370
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
6
replies
3.2k
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 50k • written 4.4 years ago by ▴ 30
4
votes
6
replies
1.2k
views
Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
17 months ago Abdul ▴ 20
1
vote
5
replies
949
views
DESEQ2 design matrix for double knockout interaction with condition
deseq2 model.matrix design matrix
updated 5.0 years ago by 41k • written 5.0 years ago by • 0
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
6.8 years ago heikki.sarin ▴ 10
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 6.0 years ago by 50k • written 6.0 years ago by • 0
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 8.0 years ago by 41k • written 8.0 years ago by • 0
4
votes
4
replies
1.7k
views
Limma Nuisance Variable in an Interaction Model
limma model.matrix
updated 8.4 years ago by ★ 7.9k • written 8.4 years ago by ▴ 370
3
votes
4
replies
1.4k
views
Paired Experimental Design
limma model.matrix
updated 8.5 years ago by 65k • written 8.5 years ago by ▴ 370
2
votes
4
replies
1.9k
views
Matrix not full rank - DESeq2
deseq2 model matrix not full rank model.matrix deseq differential binding analysis
updated 6.3 years ago by ★ 3.7k • written 6.3 years ago by ▴ 60
4
votes
4
replies
1.3k
views
edgeR: Choice of reference group in nested model
edgeR model.matrix nested design reference group
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 40
0
votes
4
replies
955
views
DESeq2 analysis design - different individuals for all samples
deseq2 rnaseq model.matrix experimental design
5.5 years ago Maithê Barros ▴ 10
3
votes
4
replies
1.4k
views
How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
2.1 years 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
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 41k • written 6.5 years ago by • 0
5
votes
3
replies
6.9k
views
Limma: Continuous variable model designs
limma model.matrix
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 370
1
vote
3
replies
1.6k
views
limma overfitting model due to intercept and yet exclusion of intercept= uninterpretable results
limma microarray linear model statistical modeling model.matrix
8.0 years ago christopher.clarskon15 ▴ 20
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 ▴ 680 • written 7.8 years ago by • 0
2
votes
3
replies
1.2k
views
Issues about experiment design
limma model.matrix makecontrasts
7.2 years ago TFony ▴ 10
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
9
votes
3
replies
5.0k
views
[limma] Define contrasts for model with covariates
limma model.matrix makecontrasts
updated 5.9 years ago by 50k • written 5.9 years ago by ▴ 660
1
vote
3
replies
904
views
Collapse Technical Replicates and Group-specific condition effects, individuals nested within groups
deseq2 RNAseq model.matrix collapseTechnicalReplicates
updated 4.4 years ago by 41k • written 4.4 years ago by ▴ 40
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
3
votes
2
replies
862
views
model matrix design for DESeq2 for use with lfcShrink function
deseq2 model.matrix
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
2
votes
2
replies
853
views
Help with constructing design matrix for edgeR/limma
limma design.matrix model.matrix edgeR
23 months ago adrianna_07 • 0
0
votes
2
replies
1.3k
views
Right use of model.matrix?
limma agilent microarray lmfit model.matrix
updated 7.5 years ago by 50k • written 7.5 years ago by ▴ 10
0
votes
2
replies
1.7k
views
Random effects metagenomeSeq
model.matrix
updated 8.2 years ago by ▴ 30 • written 8.3 years ago by • 0
1
vote
2
replies
759
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
17 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
787
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
17 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
1.8k
views
Limma model fitting: including and excluding replicates in the model gives different results in RNAseq Analysis
limma RNAseq_Analysis model.matrix
updated 8.9 years ago by ★ 28k • written 8.9 years ago by • 0
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 ★ 7.9k • written 6.1 years ago by ▴ 20
1
vote
2
replies
1.2k
views
Mixed conditions: Design and contrast matrix
limma model.matrix
updated 6.4 years ago by ★ 7.9k • written 6.4 years ago by • 0
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 arom2 • 0
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 3.9 years ago by 65k • written 3.9 years ago by • 0
0
votes
1
reply
1.4k
views
Proper dataset form and model for DEXeq analysis
dexseq rna-seq model.matrix model
updated 6.8 years ago by 41k • written 6.8 years ago by ▴ 10
0
votes
1
reply
2.2k
views
RUVseq: How to implement to more complex time-course model?
ruvseq deseq2 model.matrix confounders
updated 6.7 years ago by ▴ 950 • written 6.7 years ago by ▴ 10
1
vote
1
reply
748
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 65k • written 14 months ago by • 0
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 41k • written 6.3 years ago by ▴ 60
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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