Showing : design and contrast matrix • reset
2
votes
4
replies
2.7k
views
edgeR design matrix and contrasts for comparisons both between and within subjects
edger rnaseq design and contrast matrix
updated 5.1 years ago by 52k • written 5.1 years ago by • 0
0
votes
2
replies
1.4k
views
DESeq2 Design with Multiple Replicates of Individuals including Tumour and Normal
DESeq2 design and contrast matrix
6.3 years ago bruce.moran ▴ 30
1
vote
2
replies
1.3k
views
genes repeated in the heatmap several times(10x) when using limma
limma normalization heatmap design and contrast matrix cancer
updated 6.4 years ago by ★ 1.1k • written 6.4 years ago by • 0
5
votes
5
replies
1.8k
views
Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma design and contrast matrix design matrix contrast matrix
updated 6.4 years ago by 68k • written 6.4 years ago by ▴ 280
2
votes
2
replies
1.1k
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 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
2
votes
2
replies
1.4k
views
another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 6.8 years ago by 52k • written 6.8 years ago by • 0
3
votes
4
replies
1.5k
views
Building contrasts for combined treatment groups to compare to a control
edger design and contrast matrix
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
1
vote
5
replies
1.7k
views
p-value the same for different contrasts DESeq2
deseq2 design and contrast matrix
updated 18 days ago by • 0 • written 6.8 years ago by ▴ 10
3
votes
6
replies
1.7k
views
Design/contrast matrix for Multivariate experimental design in limma
microarray limma design and contrast matrix
updated 6.9 years ago by 52k • written 6.9 years ago by ▴ 30
0
votes
2
replies
1.2k
views
DESeq account for using two different siRNA constructs to knockdown same gene
deseq2 design and contrast matrix multiple factor design design matrix
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
1
vote
2
replies
1.1k
views
Likeliness Ratio Test
deseq2 design and contrast matrix
6.9 years ago csijst • 0
0
votes
0
replies
889
views
Limma making contrasts
limma design matrix design and contrast matrix
6.9 years ago matina • 0
1
vote
8
replies
2.4k
views
DESeq2 : group specific effect of a treatment while controlling for individual effect
deseq2 DESeq design and contrast matrix deseq
7.0 years ago SPbeginner • 0
0
votes
4
replies
2.0k
views
edgeR design matrix
edgeR design and contrast matrix design matrix
updated 7.0 years ago by 52k • written 7.0 years ago by ▴ 20
4
votes
4
replies
8.8k
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 7.1 years ago by 52k • written 7.1 years ago by ▴ 20
0
votes
0
replies
1.0k
views
Contrast matrix for a continuous covariate - for EGSEA algorithm
design and contrast matrix egsea
7.1 years ago Stefano Mangiola ▴ 40
0
votes
4
replies
2.9k
views
Contrasts & coefficients in limma
design and contrast matrix
updated 7.1 years ago by 52k • written 7.1 years ago by • 0
2
votes
5
replies
1.8k
views
DEGs generation parameters and specificities
deseq2 results design and contrast matrix
updated 7.3 years ago by 43k • written 7.9 years ago by • 0
2
votes
1
reply
1.0k
views
Is my design appropriate for contrast in DESeq2?
deseq2 design and contrast matrix rnaseq
updated 7.4 years ago by ▴ 690 • written 7.4 years ago by • 0
0
votes
2
replies
2.1k
views
Draw volcano plot by modifying contrast matrix (lumi package)
volcanoplot design and contrast matrix
updated 7.4 years ago by 52k • written 7.4 years ago by • 0
1
vote
1
reply
1.1k
views
design contrast in limma package for microarray expression data
limma design and contrast matrix differential gene expression
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 30
4
votes
3
replies
1.6k
views
edgeR design between and within subjects
edgeR design and contrast matrix
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 370
0
votes
1
reply
1.5k
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 7.5 years ago by 43k • written 7.6 years ago by ▴ 30
0
votes
2
replies
1.6k
views
DESeq2 multifactorialdesign contrasts
deseq2 rnaseq multifactorial design design and contrast matrix
updated 7.6 years ago by ▴ 690 • written 7.6 years ago by • 0
0
votes
0
replies
1.2k
views
Multiple pairwise comparisons
design and contrast matrix
7.6 years ago ucheuna • 0
2
votes
6
replies
3.4k
views
RNA-seq analysis across different experiments
limma deseq2 normalization degenes design and contrast matrix
written 7.6 years ago by ▴ 10
0
votes
0
replies
1.6k
views
design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
nanostring NanoStringDiff design and contrast matrix differential gene expression ncounter
7.6 years ago c.kohler • 0
6
votes
7
replies
2.6k
views
Multi-level experiment with limma
limma design and contrast matrix differential gene expression regression
updated 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
4
votes
8
replies
8.2k
views
DESeq2: Error in cleanContrast
deseq2 design and contrast matrix
updated 7.6 years ago by ★ 3.0k • written 7.6 years ago by • 0
7
votes
4
replies
3.2k
views
Help with design matrix for two cell types, multiple treatments
limma deseq2 design and contrast matrix
updated 7.6 years ago by • 0 • written 9.3 years ago by ▴ 90
1
vote
3
replies
1.4k
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 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
1
vote
1
reply
5.5k
views
unable to update packages: foreign, Matrix
limma design and contrast matrix
updated 7.7 years ago by 68k • written 7.7 years ago by ▴ 30
1
vote
1
reply
884
views
Diff. gene expression analysis by EdgeR
design and contrast matrix
7.8 years ago johan.vanongeval • 0
9
votes
4
replies
6.9k
views
Limma: Paired samples, multiple groups: problems understanding contrasts and model.matrix
microarray limma design and contrast matrix
7.9 years ago Anna ▴ 50
2
votes
1
reply
1.2k
views
Differences among phenotypes with different subgroups
design and contrast matrix statistical modeling edger DiffBind
updated 8.0 years ago by ★ 5.2k • written 8.0 years ago by ▴ 10
3
votes
6
replies
30k
views
Designing a contrast in DESEQ
deseq2 design and contrast matrix model matrix
8.0 years ago mrigaya.mehra ▴ 10
3
votes
4
replies
1.8k
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 8.0 years ago by 52k • written 8.0 years ago by ▴ 840
0
votes
1
reply
881
views
Contrast Specific Dispersion Estimate
edgeR design and contrast matrix
8.0 years ago tk • 0
1
vote
2
replies
1.3k
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 8.4 years ago by 68k • written 8.4 years ago by ▴ 80
3
votes
3
replies
1.3k
views
EdgeR design and contrasts questions
rnaseq edger design and contrast matrix
8.4 years ago jjh • 0
0
votes
0
replies
1.0k
views
JunctionSeq pairwise contrast with a multi-level treatment
junctionseq design and contrast matrix
8.4 years ago stuart • 0
3
votes
4
replies
2.5k
views
Deseq2 DE between WT and MUTANT normalised with respect to control
deseq2 multiple factor design design and contrast matrix design multifactorial design
8.4 years ago shimbalama • 0
4
votes
4
replies
3.0k
views
design and contrast matrix for RNA seq analysis with three different controls
bioconductor edgeR design and contrast matrix rnaseq differential gene expression
updated 8.5 years ago by ★ 28k • written 8.5 years ago by • 0
1
vote
12
replies
1.8k
views
Help for defining design and contrasts of shRNA screen data
edgeR design and contrast matrix
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 90
2
votes
6
replies
1.7k
views
edgeR - making 12 contrast but only get 5 contrasts as a result
r edger de contrast design and contrast matrix
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 300
1
vote
8
replies
2.1k
views
Understanding the design matrix
deseq2 design and contrast matrix
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 30
2
votes
6
replies
2.1k
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 8.9 years ago by 43k • written 8.9 years ago by ▴ 10
2
votes
2
replies
1.4k
views
limma making contrasts appropriately
limma design and contrast matrix
updated 8.9 years ago by ★ 13k • written 8.9 years ago by ▴ 20
2
votes
4
replies
6.1k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.9 years ago dwzhang.wisc ▴ 20
4
votes
3
replies
3.8k
views
limma: model/contrast matrix for 2x3 factorial design
limma multifactorial design design and contrast matrix limma design matrix limma contrast matrix
updated 8.9 years ago by 52k • written 8.9 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
Awards • All
Popular Question to Matthew McCormack ▴ 180
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.1k
Popular Question to Marco • 0
Popular Question to Stefano Mangiola ▴ 40
Locations • All
USA, 9 minutes ago
United States, 1 hour ago
United States, 1 hour ago
United States, 2 hours ago
China, 3 hours ago
Traffic: 1334 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6