Showing : model.matrix • reset
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358
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RUVseq how to automatically create model.matrix with all unwanted factors of variation
RUVseq model.matrix edger
updated 13 months ago by 57k • written 13 months ago by • 0
2
votes
7
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291
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Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 13 months ago by 43k • written 13 months ago by • 0
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143
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EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
19 months ago ingerslev • 0
1
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3
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173
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Collapse Technical Replicates and Group-specific condition effects, individuals nested within groups
deseq2 RNAseq model.matrix collapseTechnicalReplicates
updated 19 months ago by 33k • written 19 months ago by ▴ 20
3
votes
6
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667
views
Understanding voom behavior when model matrix is used with/without intercept for a continuous variable
limma voom rnaseq model.matrix intercept
updated 20 months ago by 43k • written 20 months ago by ▴ 30
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0
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253
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Blocking term for nested design in limma
limma mixed-effects model.matrix
22 months ago Finn • 0
1
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5
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261
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DESEQ2 design matrix for double knockout interaction with condition
deseq2 model.matrix design matrix
updated 2.2 years ago by 33k • written 2.2 years ago by • 0
3
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2
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273
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model matrix design for DESeq2 for use with lfcShrink function
deseq2 model.matrix
updated 2.4 years ago by 33k • written 2.4 years ago by • 0
4
votes
7
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1.1k
views
LIMMA time series spline model.matrix design setup
limma design model.matrix time series splines
updated 2.5 years ago by ★ 27k • written 2.5 years ago by • 0
0
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4
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313
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DESeq2 analysis design - different individuals for all samples
deseq2 rnaseq model.matrix experimental design
2.7 years ago Maithê Barros ▴ 10
1
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9
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502
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shRNA-Seq analysis using edgeR
shrnaseq edger experimental design model.matrix
updated 2.7 years ago by ★ 27k • written 2.7 years ago by ★ 1.5k
0
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6
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461
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Custom model matrix for multi factordesign
deseq2 LRT geometric mean estimatesizefactors model.matrix
updated 2.8 years ago by 33k • written 2.8 years ago by • 0
4
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3
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2.3k
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[limma] Define contrasts for model with covariates
limma model.matrix makecontrasts
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 570
4
votes
4
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649
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edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression model.matrix design matrix
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
1
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2
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401
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Study design in DESeq2
deseq2 Model matrix not full rank model.matrix study design
3.3 years ago • updated 3.2 years ago Krzysztof Kolmus ▴ 10
4
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4
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483
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edgeR: Choice of reference group in nested model
edgeR model.matrix nested design reference group
updated 3.3 years ago by ★ 27k • written 3.3 years ago by ▴ 40
4
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2
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462
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How does the function model.matrix (to define experimental design) really works ?
experimental design model.matrix edger
updated 3.3 years ago by 7.6k • written 3.3 years ago by ▴ 10
1
vote
7
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642
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model.matrix from GDS data
model.matrix lmFit eBayes GEOquery limma
3.4 years ago darthratus • 0
2
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4
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782
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Matrix not full rank - DESeq2
deseq2 model matrix not full rank model.matrix deseq differential binding analysis
updated 3.5 years ago by ★ 3.7k • written 3.5 years ago by ▴ 60
7
votes
1
reply
1.3k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 3.5 years ago by 33k • written 3.6 years ago by ▴ 60
1
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2
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584
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Mixed conditions: Design and contrast matrix
limma model.matrix
updated 3.7 years ago by 7.6k • written 3.7 years ago by • 0
1
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3
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556
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Matrix is not full rank with Multifactorial Experiment and Time course
deseq2 multiple factor design model.matrix time course
updated 3.7 years ago by 33k • written 3.7 years ago by • 0
2
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3
replies
764
views
Differential expression of nomalised and log2 transformed data in limma
limma lmfit model.matrix differential gene expression
3.9 years ago • updated 3.8 years ago stinehedensted • 0
0
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1
reply
1.2k
views
RUVseq: How to implement to more complex time-course model?
ruvseq deseq2 model.matrix confounders
updated 4.0 years ago by ▴ 870 • written 4.0 years ago by • 0
5
votes
5
replies
1.2k
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
4.0 years ago heikki.sarin • 0
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0
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746
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How construct a model for case-control time-course experiment in DEXseq?
dexseq timecourse model.matrix model
4.0 years ago heikki.sarin • 0
0
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1
reply
944
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Proper dataset form and model for DEXeq analysis
dexseq rna-seq model.matrix model
updated 4.0 years ago by 33k • written 4.0 years ago by • 0
2
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3
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662
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Issues about experiment design
limma model.matrix makecontrasts
4.4 years ago TFony ▴ 10
0
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2
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708
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Right use of model.matrix?
limma agilent microarray lmfit model.matrix
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 10
0
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2
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801
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DESeq2 Model matrix design: Merging large RNAseq projects
deseq2 model.matrix batch effect rnaseq
4.8 years ago arom2 • 0
4
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3
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642
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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 5.0 years ago by ▴ 590 • written 5.0 years ago by • 0
3
votes
10
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3.7k
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 5.1 years ago by 43k • written 5.1 years ago by ▴ 30
2
votes
11
replies
945
views
Adjusting for confounders along with paired testing using edgeR
edgeR paired samples confounders model.matrix
updated 5.1 years ago by 7.6k • written 5.1 years ago by ▴ 30
1
vote
3
replies
901
views
limma overfitting model due to intercept and yet exclusion of intercept= uninterpretable results
limma microarray linear model statistical modeling model.matrix
5.2 years ago christopher.clarskon15 ▴ 20
1
vote
4
replies
938
views
DESeq2 , model matrix with 4 factors, error: inv(): matrix appears to be singular
deseq2 multiple factor design model.matrix
updated 5.2 years ago by 33k • written 5.2 years ago by • 0
0
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2
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977
views
Random effects metagenomeSeq
model.matrix
updated 5.5 years ago by ▴ 30 • written 5.5 years ago by • 0
2
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6
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1.9k
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Understanding and creating various comparisons with model.matrix in limma regarding microarrays
limma microarray multifactorial design duplicatecorrelation model.matrix
5.6 years ago Konstantinos Yeles ▴ 60
4
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4
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1.2k
views
Limma Nuisance Variable in an Interaction Model
limma model.matrix
updated 5.6 years ago by 7.6k • written 5.6 years ago by ▴ 340
3
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4
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788
views
Paired Experimental Design
limma model.matrix
updated 5.8 years ago by 57k • written 5.8 years ago by ▴ 340
5
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3
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4.2k
views
Limma: Continuous variable model designs
limma model.matrix
updated 5.8 years ago by ★ 27k • written 5.8 years ago by ▴ 340
0
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6
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1.2k
views
DESeq2 design model-mothers & offspring timepoint comparisons
model.matrix multiple factor design design and contrast matrix deseq2
updated 5.9 years ago by 33k • written 5.9 years ago by • 0
3
votes
5
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1.2k
views
Complex Model Design with Bumphunter (Minfi)
minfi bumphunter model.matrix linear model
6.0 years ago andrew.j.skelton73 ▴ 340
1
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2
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1.2k
views
Limma model fitting: including and excluding replicates in the model gives different results in RNAseq Analysis
limma RNAseq_Analysis model.matrix
updated 6.1 years ago by ★ 27k • written 6.1 years ago by • 0
43 results • Page 1 of 1
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Comment: featureCounts - paired-end data by Yanfang • 0
Hey Wei shi, May I ask you something related to featureCounts? I have only paired end reads (RNAseq) mapping to its genome by bowtie2, an…
Comment: WGCNA adjust p value by Kevin Blighe 3.2k
Cross-posted: https://www.biostars.org/p/9482927/
Comment: Unique GPos taking into account mcols by Marcel Ramos 540
Hi @maltethodberg We currently do not have a method that does this. Perhaps a `duplicated` method is appropriate but I am not the develop…
Comment: What are these genes ? [How to get Ensembl IDs for them] by abf ▴ 30
Mouse genes are not typically all capitals, but I was able to find a reference to a mouse gene in NCBI to [CH36-217G15][1]. Maybe this is …
Comment: Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db. by abf ▴ 30
I should note that when I query org.Mm.eg.db using the gene Symbols associated with my differential expression data I find a 1:1 correspond…
Votes
A: Normalized counts of DESeq2 affected by design formula?
A: Finding orthologous human/mouse ENSEMBL IDs
Comment: What are these genes ? [How to get Ensembl IDs for them]
Answer: What lfcSE is dependent upon?
Comment: P value and Adj. P value showing N/A
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