Showing : design and contrast matrix • reset
2
votes
4
replies
3.0k
views
edgeR design matrix and contrasts for comparisons both between and within subjects
edger rnaseq design and contrast matrix
updated 5.9 years ago by 53k • written 5.9 years ago by • 0
0
votes
2
replies
1.8k
views
DESeq2 Design with Multiple Replicates of Individuals including Tumour and Normal
DESeq2 design and contrast matrix
7.0 years ago bruce.moran ▴ 30
1
vote
2
replies
1.4k
views
genes repeated in the heatmap several times(10x) when using limma
limma normalization heatmap design and contrast matrix cancer
updated 7.1 years ago by ★ 1.1k • written 7.1 years ago by • 0
5
votes
5
replies
2.2k
views
Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma design and contrast matrix design matrix contrast matrix
updated 7.2 years ago by 68k • written 7.2 years ago by ▴ 280
2
votes
2
replies
1.3k
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 7.2 years ago by ★ 29k • written 7.2 years ago by • 0
2
votes
2
replies
1.7k
views
another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 7.5 years ago by 53k • written 7.5 years ago by • 0
3
votes
4
replies
1.8k
views
Building contrasts for combined treatment groups to compare to a control
edger design and contrast matrix
updated 7.6 years ago by ★ 29k • written 7.6 years ago by • 0
1
vote
5
replies
2.0k
views
p-value the same for different contrasts DESeq2
deseq2 design and contrast matrix
updated 9 months ago by ▴ 10 • written 7.6 years ago by ▴ 10
3
votes
6
replies
2.0k
views
Design/contrast matrix for Multivariate experimental design in limma
microarray limma design and contrast matrix
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 30
0
votes
2
replies
1.4k
views
DESeq account for using two different siRNA constructs to knockdown same gene
deseq2 design and contrast matrix multiple factor design design matrix
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
1
vote
2
replies
1.3k
views
Likeliness Ratio Test
deseq2 design and contrast matrix
7.7 years ago csijst • 0
0
votes
0
replies
1.0k
views
Limma making contrasts
limma design matrix design and contrast matrix
7.7 years ago matina • 0
1
vote
8
replies
2.7k
views
DESeq2 : group specific effect of a treatment while controlling for individual effect
deseq2 DESeq design and contrast matrix deseq
7.8 years ago • updated 7.7 years ago SPbeginner • 0
0
votes
4
replies
2.4k
views
edgeR design matrix
edgeR design and contrast matrix design matrix
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 20
4
votes
4
replies
9.4k
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 7.9 years ago by 53k • written 7.9 years ago by ▴ 20
0
votes
0
replies
1.2k
views
Contrast matrix for a continuous covariate - for EGSEA algorithm
design and contrast matrix egsea
7.9 years ago Stefano Mangiola ▴ 40
1
vote
4
replies
3.2k
views
Contrasts & coefficients in limma
design and contrast matrix
updated 7.9 years ago by 53k • written 7.9 years ago by • 0
2
votes
5
replies
2.0k
views
DEGs generation parameters and specificities
deseq2 results design and contrast matrix
updated 8.1 years ago by 43k • written 8.7 years ago by • 0
2
votes
1
reply
1.2k
views
Is my design appropriate for contrast in DESeq2?
deseq2 design and contrast matrix rnaseq
updated 8.1 years ago by ▴ 690 • written 8.1 years ago by • 0
0
votes
2
replies
2.3k
views
Draw volcano plot by modifying contrast matrix (lumi package)
volcanoplot design and contrast matrix
updated 8.2 years ago by 53k • written 8.2 years ago by • 0
1
vote
1
reply
1.2k
views
design contrast in limma package for microarray expression data
limma design and contrast matrix differential gene expression
updated 8.3 years ago by ★ 29k • written 8.3 years ago by ▴ 30
4
votes
4
replies
2.0k
views
edgeR design between and within subjects
edgeR design and contrast matrix
updated 8 months ago by • 0 • written 8.3 years ago by ▴ 370
0
votes
1
reply
1.8k
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 8.3 years ago by 43k • written 8.3 years ago by ▴ 30
0
votes
2
replies
1.8k
views
DESeq2 multifactorialdesign contrasts
deseq2 rnaseq multifactorial design design and contrast matrix
updated 8.3 years ago by ▴ 690 • written 8.3 years ago by • 0
0
votes
0
replies
1.4k
views
Multiple pairwise comparisons
design and contrast matrix
8.3 years ago ucheuna • 0
2
votes
6
replies
4.0k
views
RNA-seq analysis across different experiments
limma deseq2 normalization degenes design and contrast matrix
written 8.4 years ago by ▴ 10
0
votes
0
replies
1.8k
views
design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
nanostring NanoStringDiff design and contrast matrix differential gene expression ncounter
8.4 years ago c.kohler • 0
6
votes
7
replies
2.9k
views
Multi-level experiment with limma
limma design and contrast matrix differential gene expression regression
updated 8.4 years ago by ★ 29k • written 8.4 years ago by • 0
4
votes
8
replies
8.9k
views
DESeq2: Error in cleanContrast
deseq2 design and contrast matrix
updated 8.4 years ago by ★ 3.0k • written 8.4 years ago by • 0
7
votes
4
replies
3.5k
views
Help with design matrix for two cell types, multiple treatments
limma deseq2 design and contrast matrix
updated 8.4 years ago by • 0 • written 10.1 years ago by ▴ 90
1
vote
3
replies
1.6k
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 8.4 years ago by ★ 29k • written 8.4 years ago by • 0
1
vote
1
reply
5.7k
views
unable to update packages: foreign, Matrix
limma design and contrast matrix
updated 8.5 years ago by 68k • written 8.5 years ago by ▴ 30
1
vote
1
reply
996
views
Diff. gene expression analysis by EdgeR
design and contrast matrix
8.6 years ago johan.vanongeval • 0
9
votes
4
replies
7.4k
views
Limma: Paired samples, multiple groups: problems understanding contrasts and model.matrix
microarray limma design and contrast matrix
8.7 years ago Anna ▴ 50
2
votes
1
reply
1.4k
views
Differences among phenotypes with different subgroups
design and contrast matrix statistical modeling edger DiffBind
updated 8.8 years ago by ★ 5.2k • written 8.8 years ago by ▴ 10
3
votes
6
replies
31k
views
Designing a contrast in DESEQ
deseq2 design and contrast matrix model matrix
8.8 years ago mrigaya.mehra ▴ 10
3
votes
4
replies
2.0k
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 8.8 years ago by 53k • written 8.8 years ago by ▴ 840
0
votes
1
reply
995
views
Contrast Specific Dispersion Estimate
edgeR design and contrast matrix
8.8 years ago tk • 0
1
vote
2
replies
1.5k
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 9.1 years ago by 68k • written 9.1 years ago by ▴ 90
3
votes
3
replies
1.5k
views
EdgeR design and contrasts questions
rnaseq edger design and contrast matrix
9.1 years ago jjh • 0
0
votes
0
replies
1.2k
views
JunctionSeq pairwise contrast with a multi-level treatment
junctionseq design and contrast matrix
9.1 years ago stuart • 0
3
votes
4
replies
2.8k
views
Deseq2 DE between WT and MUTANT normalised with respect to control
deseq2 multiple factor design design and contrast matrix design multifactorial design
9.2 years ago shimbalama • 0
4
votes
4
replies
3.2k
views
design and contrast matrix for RNA seq analysis with three different controls
bioconductor edgeR design and contrast matrix rnaseq differential gene expression
updated 9.3 years ago by ★ 29k • written 9.3 years ago by • 0
1
vote
12
replies
2.2k
views
Help for defining design and contrasts of shRNA screen data
edgeR design and contrast matrix
updated 9.3 years ago by ★ 29k • written 9.3 years ago by ▴ 90
2
votes
6
replies
1.9k
views
edgeR - making 12 contrast but only get 5 contrasts as a result
r edger de contrast design and contrast matrix
updated 9.5 years ago by ★ 29k • written 9.5 years ago by ▴ 300
1
vote
8
replies
2.4k
views
Understanding the design matrix
deseq2 design and contrast matrix
updated 9.6 years ago by 43k • written 9.6 years ago by ▴ 30
2
votes
6
replies
2.4k
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 9.6 years ago by 43k • written 9.6 years ago by ▴ 10
2
votes
2
replies
1.5k
views
limma making contrasts appropriately
limma design and contrast matrix
updated 9.7 years ago by ★ 13k • written 9.7 years ago by ▴ 20
2
votes
4
replies
6.6k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
9.7 years ago dwzhang.wisc ▴ 20
4
votes
3
replies
4.0k
views
limma: model/contrast matrix for 2x3 factorial design
limma multifactorial design design and contrast matrix limma design matrix limma contrast matrix
updated 9.7 years ago by 53k • written 9.7 years ago by • 0
83 results • Page 1 of 2
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Locations • All
The city by the bay, 5 minutes ago
United States, 27 minutes ago
United States, 30 minutes ago
WEHI, Melbourne, Australia, 4 hours ago
Seattle, WA, United States, 6 hours ago
Traffic: 1210 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