Showing : design and contrast matrix • reset
2
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4
replies
217
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edgeR design matrix and contrasts for comparisons both between and within subjects
edger rnaseq design and contrast matrix
updated 17 months ago by 43k • written 17 months ago by • 0
0
votes
2
replies
334
views
DESeq2 Design with Multiple Replicates of Individuals including Tumour and Normal
DESeq2 design and contrast matrix
2.6 years ago bruce.moran ▴ 30
1
vote
2
replies
407
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genes repeated in the heatmap several times(10x) when using limma
limma normalization heatmap design and contrast matrix cancer
updated 2.7 years ago by ▴ 980 • written 2.7 years ago by • 0
5
votes
5
replies
536
views
Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma design and contrast matrix design matrix contrast matrix
updated 2.7 years ago by 57k • written 2.7 years ago by ▴ 230
2
votes
2
replies
346
views
Correct formulation of contrasts of interest regarding an RNA-Seq gene expression analysis with edgeR
rnaseq edger design and contrast matrix multifactorial design
updated 2.8 years ago by ★ 26k • written 2.8 years ago by • 0
2
votes
2
replies
457
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another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
3
votes
4
replies
507
views
Building contrasts for combined treatment groups to compare to a control
edger design and contrast matrix
updated 3.1 years ago by ★ 26k • written 3.1 years ago by • 0
1
vote
4
replies
675
views
p-value the same for different contrasts DESeq2
deseq2 design and contrast matrix
updated 3.1 years ago by 33k • written 3.1 years ago by ▴ 10
3
votes
6
replies
626
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Design/contrast matrix for Multivariate experimental design in limma
microarray limma design and contrast matrix
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
votes
2
replies
467
views
DESeq account for using two different siRNA constructs to knockdown same gene
deseq2 design and contrast matrix multiple factor design design matrix
updated 3.2 years ago by 33k • written 3.2 years ago by • 0
1
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2
replies
386
views
Likeliness Ratio Test
deseq2 design and contrast matrix
3.2 years ago csijst • 0
0
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0
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329
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Limma making contrasts
limma design matrix design and contrast matrix
3.2 years ago matina • 0
1
vote
8
replies
1.2k
views
DESeq2 : group specific effect of a treatment while controlling for individual effect
deseq2 DESeq design and contrast matrix deseq
3.3 years ago SPbeginner • 0
0
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4
replies
679
views
edgeR design matrix
edgeR design and contrast matrix design matrix
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 20
2
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4
replies
3.7k
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 3.4 years ago by 43k • written 3.4 years ago by ▴ 20
0
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0
replies
349
views
Contrast matrix for a continuous covariate - for EGSEA algorithm
design and contrast matrix egsea
3.4 years ago stefano.mangiola • 0
0
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4
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1.3k
views
Contrasts & coefficients in limma
design and contrast matrix
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
2
votes
5
replies
987
views
DEGs generation parameters and specificities
deseq2 results design and contrast matrix
updated 3.6 years ago by 33k • written 4.2 years ago by • 0
2
votes
1
reply
415
views
Is my design appropriate for contrast in DESeq2?
deseq2 design and contrast matrix rnaseq
updated 3.7 years ago by ▴ 590 • written 3.7 years ago by • 0
0
votes
2
replies
915
views
Draw volcano plot by modifying contrast matrix (lumi package)
volcanoplot design and contrast matrix
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
1
vote
1
reply
617
views
design contrast in limma package for microarray expression data
limma design and contrast matrix differential gene expression
updated 3.8 years ago by ★ 26k • written 3.8 years ago by ▴ 30
3
votes
3
replies
763
views
edgeR design between and within subjects
edgeR design and contrast matrix
updated 3.8 years ago by ★ 26k • written 3.8 years ago by ▴ 340
0
votes
1
reply
772
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 3.8 years ago by 33k • written 3.9 years ago by ▴ 30
0
votes
2
replies
921
views
DESeq2 multifactorialdesign contrasts
deseq2 rnaseq multifactorial design design and contrast matrix
updated 3.9 years ago by ▴ 590 • written 3.9 years ago by • 0
0
votes
0
replies
706
views
Multiple pairwise comparisons
design and contrast matrix
3.9 years ago ucheuna • 0
2
votes
5
replies
1.2k
views
RNA-seq analysis across different experiments
limma deseq2 normalization degenes design and contrast matrix
updated 3.9 years ago by ▴ 50 • written 3.9 years ago by ▴ 10
0
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0
replies
638
views
design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
nanostring NanoStringDiff design and contrast matrix differential gene expression ncounter
3.9 years ago c.kohler • 0
6
votes
7
replies
1.0k
views
Multi-level experiment with limma
limma design and contrast matrix differential gene expression regression
updated 3.9 years ago by ★ 26k • written 3.9 years ago by • 0
4
votes
8
replies
2.1k
views
DESeq2: Error in cleanContrast
deseq2 design and contrast matrix
updated 3.9 years ago by ★ 2.6k • written 3.9 years ago by • 0
7
votes
4
replies
2.0k
views
Help with design matrix for two cell types, multiple treatments
limma deseq2 design and contrast matrix
updated 4.0 years ago by • 0 • written 5.6 years ago by ▴ 70
1
vote
3
replies
541
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 4.0 years ago by ★ 26k • written 4.0 years ago by • 0
1
vote
1
reply
4.1k
views
unable to update packages: foreign, Matrix
limma design and contrast matrix
updated 4.0 years ago by 57k • written 4.0 years ago by ▴ 30
1
vote
1
reply
503
views
Diff. gene expression analysis by EdgeR
design and contrast matrix
4.1 years ago johan.vanongeval • 0
9
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4
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3.8k
views
Limma: Paired samples, multiple groups: problems understanding contrasts and model.matrix
microarray limma design and contrast matrix
4.2 years ago Anna ▴ 50
2
votes
1
reply
552
views
Differences among phenotypes with different subgroups
design and contrast matrix statistical modeling edger DiffBind
updated 4.3 years ago by ★ 3.9k • written 4.3 years ago by ▴ 10
3
votes
6
replies
6.2k
views
Designing a contrast in DESEQ
deseq2 design and contrast matrix model matrix
4.3 years ago mrigaya.mehra ▴ 10
3
votes
4
replies
893
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 4.3 years ago by 43k • written 4.4 years ago by ▴ 780
0
votes
1
reply
425
views
Contrast Specific Dispersion Estimate
edgeR design and contrast matrix
4.4 years ago tk • 0
0
votes
2
replies
604
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 4.7 years ago by 57k • written 4.7 years ago by ▴ 60
3
votes
3
replies
578
views
EdgeR design and contrasts questions
rnaseq edger design and contrast matrix
4.7 years ago jjh • 0
0
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0
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413
views
JunctionSeq pairwise contrast with a multi-level treatment
junctionseq design and contrast matrix
4.7 years ago stuart • 0
3
votes
4
replies
890
views
Deseq2 DE between WT and MUTANT normalised with respect to control
deseq2 multiple factor design design and contrast matrix design multifactorial design
4.8 years ago • updated 4.7 years ago shimbalama • 0
4
votes
4
replies
1.2k
views
design and contrast matrix for RNA seq analysis with three different controls
bioconductor edgeR design and contrast matrix rnaseq differential gene expression
updated 4.8 years ago by ★ 26k • written 4.8 years ago by • 0
1
vote
12
replies
713
views
Help for defining design and contrasts of shRNA screen data
edgeR design and contrast matrix
updated 4.8 years ago by ★ 26k • written 4.8 years ago by ▴ 90
2
votes
6
replies
748
views
edgeR - making 12 contrast but only get 5 contrasts as a result
r edger de contrast design and contrast matrix
updated 5.0 years ago by ★ 26k • written 5.0 years ago by ▴ 290
1
vote
8
replies
829
views
Understanding the design matrix
deseq2 design and contrast matrix
updated 5.1 years ago by 33k • written 5.1 years ago by ▴ 30
2
votes
6
replies
1.0k
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 5.2 years ago by 33k • written 5.2 years ago by ▴ 10
2
votes
2
replies
723
views
limma making contrasts appropriately
limma design and contrast matrix
updated 5.2 years ago by 13k • written 5.2 years ago by ▴ 20
2
votes
4
replies
3.0k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
5.2 years ago dwzhang.wisc ▴ 20
4
votes
3
replies
2.0k
views
limma: model/contrast matrix for 2x3 factorial design
limma multifactorial design design and contrast matrix limma design matrix limma contrast matrix
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
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Answer: change text size in plotmd functtion by Gordon Smyth 43k
Do you mean the text in the legend? Anyway, just make the dimensions of your graphics window smaller, then all text and points in the plot …
Comment: Annotation using QSEA package by rtrivedi1 ▴ 10
Issue is fixed now !! Thanks Rakesh
Comment: Binding matrix created by DiffBind by sh.kazempour94 ▴ 10
Thank you for helping me figuring this out! The matrix from dba.peakset() seems to be the correct one. Thanks!
Comment: Annotation using QSEA package by James W. MacDonald 57k
OK. This is the part I meant about using an accessor. There is a function called `genome` that does what you have tried to do. It actually …
Comment: Annotation using QSEA package by rtrivedi1 ▴ 10
Hi, Step 1: I used the following code to get hg38_anno_final: ``` library(annotatr) library(TxDb.Hsapiens.UCSC.hg38.knownGene) hg38_ann…
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Comment: Annotation using QSEA package
Comment: Binding matrix created by DiffBind
Comment: Annotation using QSEA package
Answer: Annotation using QSEA package
Answer: lmFit, number of proteins
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