Showing : design and contrast matrix • reset
2
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4
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273
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edgeR design matrix and contrasts for comparisons both between and within subjects
edger rnaseq design and contrast matrix
updated 20 months ago by 43k • written 20 months ago by • 0
0
votes
2
replies
363
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DESeq2 Design with Multiple Replicates of Individuals including Tumour and Normal
DESeq2 design and contrast matrix
2.8 years ago bruce.moran ▴ 30
1
vote
2
replies
505
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genes repeated in the heatmap several times(10x) when using limma
limma normalization heatmap design and contrast matrix cancer
updated 2.9 years ago by ▴ 980 • written 2.9 years ago by • 0
5
votes
5
replies
577
views
Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma design and contrast matrix design matrix contrast matrix
updated 3.0 years ago by 58k • written 3.0 years ago by ▴ 230
2
votes
2
replies
373
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Correct formulation of contrasts of interest regarding an RNA-Seq gene expression analysis with edgeR
rnaseq edger design and contrast matrix multifactorial design
updated 3.0 years ago by ★ 27k • written 3.0 years ago by • 0
2
votes
2
replies
502
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another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
3
votes
4
replies
550
views
Building contrasts for combined treatment groups to compare to a control
edger design and contrast matrix
updated 3.4 years ago by ★ 27k • written 3.4 years ago by • 0
1
vote
4
replies
742
views
p-value the same for different contrasts DESeq2
deseq2 design and contrast matrix
updated 3.4 years ago by 34k • written 3.4 years ago by ▴ 10
3
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6
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702
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Design/contrast matrix for Multivariate experimental design in limma
microarray limma design and contrast matrix
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
votes
2
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501
views
DESeq account for using two different siRNA constructs to knockdown same gene
deseq2 design and contrast matrix multiple factor design design matrix
updated 3.4 years ago by 34k • written 3.4 years ago by • 0
1
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2
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430
views
Likeliness Ratio Test
deseq2 design and contrast matrix
3.5 years ago csijst • 0
0
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0
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355
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Limma making contrasts
limma design matrix design and contrast matrix
3.5 years ago matina • 0
1
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8
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1.3k
views
DESeq2 : group specific effect of a treatment while controlling for individual effect
deseq2 DESeq design and contrast matrix deseq
3.5 years ago SPbeginner • 0
0
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4
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747
views
edgeR design matrix
edgeR design and contrast matrix design matrix
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 20
2
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4
replies
4.1k
views
edgeR design matrix and contrasts: how to make contrast between groups that aren't shown in the design matrix columns?
edger design and contrast matrix contrast limma contrast matrix limma
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 20
0
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0
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382
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Contrast matrix for a continuous covariate - for EGSEA algorithm
design and contrast matrix egsea
3.7 years ago stefano.mangiola • 0
0
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4
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1.4k
views
Contrasts & coefficients in limma
design and contrast matrix
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
2
votes
5
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1.0k
views
DEGs generation parameters and specificities
deseq2 results design and contrast matrix
updated 3.9 years ago by 34k • written 4.4 years ago by • 0
2
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1
reply
445
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Is my design appropriate for contrast in DESeq2?
deseq2 design and contrast matrix rnaseq
updated 3.9 years ago by ▴ 590 • written 3.9 years ago by • 0
0
votes
2
replies
981
views
Draw volcano plot by modifying contrast matrix (lumi package)
volcanoplot design and contrast matrix
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
1
vote
1
reply
640
views
design contrast in limma package for microarray expression data
limma design and contrast matrix differential gene expression
updated 4.1 years ago by ★ 27k • written 4.1 years ago by ▴ 30
3
votes
3
replies
807
views
edgeR design between and within subjects
edgeR design and contrast matrix
updated 4.1 years ago by ★ 27k • written 4.1 years ago by ▴ 340
0
votes
1
reply
805
views
Analyze time course experiment with multiple samples from multiple animals with DESeq2
deseq2 multiple factor design multifactorial design multiple time points design and contrast matrix
updated 4.1 years ago by 34k • written 4.1 years ago by ▴ 30
0
votes
2
replies
963
views
DESeq2 multifactorialdesign contrasts
deseq2 rnaseq multifactorial design design and contrast matrix
updated 4.1 years ago by ▴ 590 • written 4.1 years ago by • 0
0
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0
replies
741
views
Multiple pairwise comparisons
design and contrast matrix
4.1 years ago ucheuna • 0
2
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5
replies
1.3k
views
RNA-seq analysis across different experiments
limma deseq2 normalization degenes design and contrast matrix
updated 4.1 years ago by ▴ 50 • written 4.1 years ago by ▴ 10
0
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0
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695
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design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
nanostring NanoStringDiff design and contrast matrix differential gene expression ncounter
4.2 years ago c.kohler • 0
6
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7
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1.1k
views
Multi-level experiment with limma
limma design and contrast matrix differential gene expression regression
updated 4.2 years ago by ★ 27k • written 4.2 years ago by • 0
4
votes
8
replies
2.3k
views
DESeq2: Error in cleanContrast
deseq2 design and contrast matrix
updated 4.2 years ago by ★ 2.6k • written 4.2 years ago by • 0
7
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4
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2.1k
views
Help with design matrix for two cell types, multiple treatments
limma deseq2 design and contrast matrix
updated 4.2 years ago by • 0 • written 5.8 years ago by ▴ 90
1
vote
3
replies
570
views
Limma: model Design matrix and contrast matrix for getting gene log2 fold change data
bioconductor affymetrix microarrays differential gene expression design and contrast matrix
updated 4.2 years ago by ★ 27k • written 4.2 years ago by • 0
1
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1
reply
4.1k
views
unable to update packages: foreign, Matrix
limma design and contrast matrix
updated 4.3 years ago by 58k • written 4.3 years ago by ▴ 30
1
vote
1
reply
524
views
Diff. gene expression analysis by EdgeR
design and contrast matrix
4.4 years ago johan.vanongeval • 0
9
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4
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4.1k
views
Limma: Paired samples, multiple groups: problems understanding contrasts and model.matrix
microarray limma design and contrast matrix
4.5 years ago Anna ▴ 50
2
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1
reply
583
views
Differences among phenotypes with different subgroups
design and contrast matrix statistical modeling edger DiffBind
updated 4.5 years ago by ★ 4.1k • written 4.5 years ago by ▴ 10
3
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6
replies
7.8k
views
Designing a contrast in DESEQ
deseq2 design and contrast matrix model matrix
4.6 years ago mrigaya.mehra ▴ 10
3
votes
4
replies
942
views
Appropriate design matrix set up in limma for 2-factor approches with NA values for specific levels
limma multiple factor design NA values design and contrast matrix
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 780
0
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1
reply
451
views
Contrast Specific Dispersion Estimate
edgeR design and contrast matrix
4.6 years ago tk • 0
0
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2
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637
views
Correct construction of multiple design matrix with limma in an agilent microarray dataset
limma multiple factor design multiple time points microarray design and contrast matrix
updated 4.9 years ago by 58k • written 4.9 years ago by ▴ 70
3
votes
3
replies
618
views
EdgeR design and contrasts questions
rnaseq edger design and contrast matrix
4.9 years ago jjh • 0
0
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0
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441
views
JunctionSeq pairwise contrast with a multi-level treatment
junctionseq design and contrast matrix
4.9 years ago stuart • 0
3
votes
4
replies
984
views
Deseq2 DE between WT and MUTANT normalised with respect to control
deseq2 multiple factor design design and contrast matrix design multifactorial design
5.0 years ago shimbalama • 0
4
votes
4
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1.3k
views
design and contrast matrix for RNA seq analysis with three different controls
bioconductor edgeR design and contrast matrix rnaseq differential gene expression
updated 5.1 years ago by ★ 27k • written 5.1 years ago by • 0
1
vote
12
replies
785
views
Help for defining design and contrasts of shRNA screen data
edgeR design and contrast matrix
updated 5.1 years ago by ★ 27k • written 5.1 years ago by ▴ 90
2
votes
6
replies
796
views
edgeR - making 12 contrast but only get 5 contrasts as a result
r edger de contrast design and contrast matrix
updated 5.3 years ago by ★ 27k • written 5.3 years ago by ▴ 290
1
vote
8
replies
883
views
Understanding the design matrix
deseq2 design and contrast matrix
updated 5.4 years ago by 34k • written 5.4 years ago by ▴ 30
2
votes
6
replies
1.1k
views
Seeking confirmation on manually setting contrasts for a 3-factor design in DESeq2 with multiple interaction terms
deseq2 multiple factor design interactions design and contrast matrix contrast
updated 5.4 years ago by 34k • written 5.4 years ago by ▴ 10
2
votes
2
replies
756
views
limma making contrasts appropriately
limma design and contrast matrix
updated 5.4 years ago by 13k • written 5.5 years ago by ▴ 20
2
votes
4
replies
3.3k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
5.5 years ago dwzhang.wisc ▴ 20
4
votes
3
replies
2.1k
views
limma: model/contrast matrix for 2x3 factorial design
limma multifactorial design design and contrast matrix limma design matrix limma contrast matrix
updated 5.5 years ago by 43k • written 5.5 years ago by • 0
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Comment: Returning to edgeR version 3.26.1? by mvanhorn • 0
Thank you very much for your reply! Our project is a reanalysis of large sets of RNA-seq data to identify circular RNAs using the CIRIquan…
Comment: "full model matrix is less than full rank" by ATpoint ▴ 840
My best guess is that young and old are not "young" or "old" but include some hidden whitespaces like " young" or "old ". That would then m…
Answer: Reading vcf file with readVcf by James W. MacDonald 58k
Usually when you run out of RAM, you usually get an error saying that 'R couldn't allocate a vector of size <some number>'. When it just sa…
Answer: Genic annotations of whole hg38 by James W. MacDonald 58k
What exactly do you mean by 'proportion of genic annotations'? One possibility would be to see what proportion of all the exons are covered…
Answer: Understanding output of Negative Binomial in DESeq2 by Michael Love 34k
> Does this mean that there are seven genes in total that will have significant adjusted p-value? yes > i recall when multiple linea…
Votes
Answer: Swish direction of comparison based on order of factors
Comment: Gradient dotplot
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Answer: Effect size using likelihood ratio test in DESeq2
Comment: ggtree install
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