Showing : design and contrast matrix • reset
7
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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
2
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6
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2.5k
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RNA-seq analysis across different experiments
limma deseq2 normalization degenes design and contrast matrix
written 6.8 years ago by ▴ 10
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5
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2.0k
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limma paired design matrix 3 factors
limma paired design and contrast matrix
9.5 years ago wim.trypsteen • 0
0
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5
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3.3k
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coefficients meaning in time course analysis with DESeq2
deseq2 timecourse time course design and contrast matrix coefficient of variation
updated 8.5 years ago by 42k • written 8.5 years ago by ★ 1.5k
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6
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6.0k
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DESeq2 design model for treatment analysis controlling for age and sex
deseq2 design and contrast matrix
9.4 years ago newmanss • 0
2
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3
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2.2k
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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
1
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2
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1.0k
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genes repeated in the heatmap several times(10x) when using limma
limma normalization heatmap design and contrast matrix cancer
updated 5.5 years ago by ★ 1.0k • written 5.5 years ago by • 0
2
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6
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1.4k
views
Limma; design matrix for treatments and sibship
limma design and contrast matrix
8.6 years ago John ▴ 10
1
vote
8
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1.6k
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Understanding the design matrix
deseq2 design and contrast matrix
updated 8.0 years ago by 42k • written 8.0 years ago by ▴ 30
3
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16
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4.1k
views
limma contrast matrix
limma contrast design and contrast matrix
9.5 years ago Smith H. ▴ 20
4
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2
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2.3k
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DESeq2 results example
deseq2 design and contrast matrix
8.9 years ago Aggarwal, Praful ▴ 50
1
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2
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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
8
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9
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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
4
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8
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6.8k
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DESeq2: Error in cleanContrast
deseq2 design and contrast matrix
updated 6.8 years ago by ★ 3.0k • written 6.8 years ago by • 0
3
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5
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1.8k
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Limma contrast matrix question/concern
limma block design and contrast matrix
8.9 years ago choofd • 0
0
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2
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1.7k
views
Draw volcano plot by modifying contrast matrix (lumi package)
volcanoplot design and contrast matrix
updated 6.6 years ago by 50k • written 6.6 years ago by • 0
10
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9
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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
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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
2
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4
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5.4k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.1 years ago dwzhang.wisc ▴ 20
2
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2
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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
4
votes
4
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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
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3
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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
2
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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
1
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12
replies
1.4k
views
Help for defining design and contrasts of shRNA screen data
edgeR design and contrast matrix
updated 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 90
4
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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
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
1
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2
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1.1k
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 7.5 years ago by 65k • written 7.5 years ago by ▴ 80
3
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4
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1.5k
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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
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
2
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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
4
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3
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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
0
votes
2
replies
1.4k
views
DE genes over time with DESeq2
deseq2 timecourse design and contrast matrix
updated 8 weeks ago by ▴ 10 • written 8.5 years ago by ★ 1.5k
3
votes
3
replies
1.1k
views
EdgeR design and contrasts questions
rnaseq edger design and contrast matrix
7.6 years ago jjh • 0
2
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5
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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
3
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4
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3.0k
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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
2
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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
1
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2
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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 9.4 years ago by ▴ 130
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
1
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2
replies
1.4k
views
Same number of topTags reported for different contrasts
edger topTags design and contrast matrix
updated 9.1 years ago by 50k • written 9.1 years ago by • 0
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
1.7k
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
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
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
12
votes
20
replies
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
1
vote
1
reply
876
views
not enough replicates to analyze significant differential expression?
limma design and contrast matrix
updated 8.6 years ago by 50k • written 8.6 years ago by • 0
13
votes
3
replies
12k
views
Understanding contrasts limma
limma design and contrast matrix
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 60
0
votes
1
reply
1.6k
views
DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2 design and contrast matrix interactions contrast
updated 8.6 years ago by 42k • written 8.6 years ago by ▴ 20
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
50 results • Page 1 of 1
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Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by Gordon Smyth 50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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