Showing : design and contrast matrix • reset
13
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3
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12k
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Understanding contrasts limma
limma design and contrast matrix
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 60
12
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20
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2.0k
views
Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma multifactorial design design and contrast matrix affymetrix microarrays
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 830
10
votes
9
replies
3.9k
views
EdgeR Multifactorial design with batch effect-trouble with defining contrasts
edger design and contrast matrix multiple factor design multiple comparisons
updated 8.9 years ago by 65k • written 8.9 years ago by ▴ 20
9
votes
4
replies
6.3k
views
Limma: Paired samples, multiple groups: problems understanding contrasts and model.matrix
microarray limma design and contrast matrix
7.1 years ago Anna ▴ 50
9
votes
7
replies
5.2k
views
Limma time series spline help
limma spline design and contrast matrix covariate
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 30
8
votes
9
replies
4.4k
views
DESeq2: Compare expression of one group to the mean of others
deseq2 heterosis contrast design and contrast matrix
updated 8.9 years ago by 42k • written 8.9 years ago by ▴ 10
7
votes
4
replies
2.9k
views
Help with design matrix for two cell types, multiple treatments
limma deseq2 design and contrast matrix
updated 6.8 years ago by • 0 • written 8.5 years ago by ▴ 90
6
votes
7
replies
2.1k
views
Multi-level experiment with limma
limma design and contrast matrix differential gene expression regression
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
6
votes
3
replies
5.5k
views
Calculating contrasts for continuous variable anad interaction effect in Limma
limma design matrix design and contrast matrix continuous interactions
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 20
5
votes
5
replies
9.2k
views
How to make contrast table to combine two conditions/treatments against another one (in a multi groups experiments
limma design and contrast matrix
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 20
5
votes
5
replies
1.4k
views
Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma design and contrast matrix design matrix contrast matrix
updated 5.6 years ago by 65k • written 5.6 years ago by ▴ 270
4
votes
4
replies
8.1k
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 6.3 years ago by 50k • written 6.3 years ago by ▴ 20
4
votes
4
replies
1.5k
views
Setting contrasts in limma where null hypothesis is that Test = 2 x Control
differential gene expression limma rnaseq design and contrast matrix limma voom
8.3 years ago stuart ▴ 10
4
votes
3
replies
3.3k
views
limma: model/contrast matrix for 2x3 factorial design
limma multifactorial design design and contrast matrix limma design matrix limma contrast matrix
updated 8.1 years ago by 50k • written 8.1 years ago by • 0
4
votes
3
replies
1.4k
views
edgeR design between and within subjects
edgeR design and contrast matrix
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 360
4
votes
4
replies
2.7k
views
design and contrast matrix for RNA seq analysis with three different controls
bioconductor edgeR design and contrast matrix rnaseq differential gene expression
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
4
votes
8
replies
6.8k
views
DESeq2: Error in cleanContrast
deseq2 design and contrast matrix
updated 6.8 years ago by ★ 3.0k • written 6.8 years ago by • 0
4
votes
2
replies
2.3k
views
DESeq2 results example
deseq2 design and contrast matrix
8.9 years ago Aggarwal, Praful ▴ 50
4
votes
8
replies
1.9k
views
EdgeR: batches and samples over-specify system, how to contrast un-modeled variables?
edger glmlrt() differential expression design and contrast matrix
updated 8.9 years ago by 50k • written 8.9 years ago by • 0
3
votes
6
replies
1.4k
views
Design/contrast matrix for Multivariate experimental design in limma
microarray limma design and contrast matrix
updated 6.1 years ago by 50k • written 6.1 years ago by ▴ 30
3
votes
4
replies
3.0k
views
Probem in defining the design matrix for RNA-Seq analysis with edgeR
edger design and contrast matrix rnaseq
updated 9.5 years ago by ★ 28k • written 9.5 years ago by ▴ 20
3
votes
4
replies
2.1k
views
Deseq2 DE between WT and MUTANT normalised with respect to control
deseq2 multiple factor design design and contrast matrix design multifactorial design
7.6 years ago shimbalama • 0
3
votes
4
replies
1.2k
views
Building contrasts for combined treatment groups to compare to a control
edger design and contrast matrix
updated 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
3
votes
16
replies
4.1k
views
limma contrast matrix
limma contrast design and contrast matrix
9.5 years ago Smith H. ▴ 20
3
votes
3
replies
1.1k
views
EdgeR design and contrasts questions
rnaseq edger design and contrast matrix
7.6 years ago jjh • 0
3
votes
5
replies
1.8k
views
Limma contrast matrix question/concern
limma block design and contrast matrix
8.9 years ago choofd • 0
3
votes
6
replies
1.7k
views
Design that evaluates response to continuous and categorical variables
limma design and contrast matrix design matrix limma design matrix
updated 8.9 years ago by 65k • written 8.9 years ago by ▴ 10
3
votes
6
replies
27k
views
Designing a contrast in DESEQ
deseq2 design and contrast matrix model matrix
7.2 years ago mrigaya.mehra ▴ 10
3
votes
4
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1.3k
views
limma design matrix question
limma design and contrast matrix limma design matrix
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 30
3
votes
4
replies
1.5k
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 7.2 years ago by 50k • written 7.2 years ago by ▴ 830
2
votes
4
replies
2.1k
views
edgeR design matrix and contrasts for comparisons both between and within subjects
edger rnaseq design and contrast matrix
updated 4.3 years ago by 50k • written 4.3 years ago by • 0
2
votes
5
replies
1.5k
views
DEGs generation parameters and specificities
deseq2 results design and contrast matrix
updated 6.5 years ago by 42k • written 7.1 years ago by • 0
2
votes
1
reply
4.0k
views
Yet another DESeq2 nested design contrast matrix question
deseq2 design and contrast matrix
9.5 years ago Darya Vanichkina ▴ 120
2
votes
3
replies
2.2k
views
edgeR paired test with batch effect
edger design and contrast matrix
updated 9.4 years ago by 50k • written 9.4 years ago by ▴ 60
2
votes
2
replies
3.0k
views
DESeq2 design matrix for 6 groups
rnaseq deseq2 design and contrast matrix
updated 9.3 years ago by 42k • written 9.3 years ago by ▴ 20
2
votes
6
replies
1.4k
views
Limma; design matrix for treatments and sibship
limma design and contrast matrix
8.6 years ago John ▴ 10
2
votes
2
replies
1.3k
views
limma:question on design for (paired?) 2 dye experiment
limma limma design matrix design and contrast matrix 2-dye
updated 8.5 years ago by 50k • written 8.5 years ago by ★ 3.9k
2
votes
4
replies
5.4k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.1 years ago dwzhang.wisc ▴ 20
2
votes
2
replies
1.2k
views
limma making contrasts appropriately
limma design and contrast matrix
updated 8.1 years ago by ★ 13k • written 8.1 years ago by ▴ 20
2
votes
6
replies
1.8k
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 8.0 years ago by 42k • written 8.0 years ago by ▴ 10
2
votes
6
replies
1.4k
views
edgeR - making 12 contrast but only get 5 contrasts as a result
r edger de contrast design and contrast matrix
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 300
2
votes
1
reply
1.0k
views
Differences among phenotypes with different subgroups
design and contrast matrix statistical modeling edger DiffBind
updated 7.2 years ago by ★ 5.2k • written 7.2 years ago by ▴ 10
2
votes
6
replies
2.5k
views
RNA-seq analysis across different experiments
limma deseq2 normalization degenes design and contrast matrix
written 6.8 years ago by ▴ 10
2
votes
1
reply
870
views
Is my design appropriate for contrast in DESeq2?
deseq2 design and contrast matrix rnaseq
updated 6.5 years ago by ▴ 680 • written 6.5 years ago by • 0
2
votes
2
replies
1.2k
views
another contrast question - edgeR + scRNA-seq + timecourse
edger single cell design and contrast matrix timecourse
updated 6.0 years ago by 50k • written 6.0 years ago by • 0
2
votes
2
replies
844
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 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
1
vote
2
replies
1.7k
views
array quality control, affy probes, contracts setting in limma, result interpretation and weights
limma affy probe qualitycontrol design and contrast matrix
updated 9.3 years ago by 50k • written 9.3 years ago by ▴ 130
1
vote
4
replies
1.4k
views
p-value the same for different contrasts DESeq2
deseq2 design and contrast matrix
updated 6.0 years ago by 42k • written 6.0 years ago by ▴ 10
1
vote
1
reply
764
views
Diff. gene expression analysis by EdgeR
design and contrast matrix
7.0 years ago johan.vanongeval • 0
1
vote
2
replies
1.7k
views
edgeR design matrix question
edgeR limma rnaseq design and contrast matrix
updated 9.4 years ago by 50k • written 9.4 years ago by • 0
50 results • Page 1 of 1
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
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Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
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