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
1.7k
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
9
replies
1.5k
views
shRNA-Seq analysis using edgeR
shrnaseq edger experimental design model.matrix
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ★ 1.5k
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 ★ 28k • written 5.2 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
1.9k
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
1.7k
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
978
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 13 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
16 months ago Abdul ▴ 20
1
vote
5
replies
935
views
DESEQ2 design matrix for double knockout interaction with condition
deseq2 model.matrix design matrix
updated 4.9 years ago by 41k • written 4.9 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
6.7 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 5.9 years ago by 50k • written 5.9 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 7.9 years ago by 41k • written 7.9 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
1.8k
views
Matrix not full rank - DESeq2
deseq2 model matrix not full rank model.matrix deseq differential binding analysis
updated 6.3 years ago by ★ 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 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 40
0
votes
4
replies
941
views
DESeq2 analysis design - different individuals for all samples
deseq2 rnaseq model.matrix experimental design
5.4 years ago Maithê Barros ▴ 10
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
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 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 370
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
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
7.1 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 5.8 years ago by 50k • written 5.8 years ago by ▴ 660
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 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
857
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
838
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
744
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
16 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
779
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
2
replies
1.7k
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 • updated 7.5 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 3.8 years ago by 65k • written 3.8 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
2.1k
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
738
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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Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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