Showing : DESIGN • reset
7
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7
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DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2 LRT rnaseq design reduced model
updated 5.4 years ago by • 0 • written 7.0 years ago by ▴ 50
6
votes
6
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2.8k
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design matrix for 4 groups in edgeR
edger design
9.5 years ago alakatos ▴ 130
6
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11
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1.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
14 months ago mohammedtoufiq91 ▴ 10
6
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6
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1.2k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 4.2 years ago by ★ 13k • written 4.2 years ago by • 0
5
votes
6
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1.5k
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How to set up appropriate analysis using sample type and condition for DESeq2
deseq2 differential gene expression design
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
4
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7
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1.1k
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 3.8 years ago by 50k • written 3.8 years ago by • 0
4
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5
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2.9k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 3.7 years ago by 65k • written 3.7 years ago by • 0
4
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3
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6.9k
views
deseq2 warning for the design formula
deseq2 design
updated 8.2 years ago by 41k • written 8.2 years ago by ★ 1.5k
4
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13
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2.5k
views
Which formula should I use to set the best model matrix for my analysis ?
DESEQ2 EDGER design
7.5 years ago ZheFrench ▴ 40
4
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7
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3.1k
views
LIMMA time series spline model.matrix design setup
limma design model.matrix time series splines
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
4
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18
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24k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 4.8 years ago by • 0 • written 9.5 years ago by ▴ 100
3
votes
3
replies
782
views
Extracting within subject effect in a between and within subject model with DESeq2
deseq2 design
updated 5.0 years ago by 41k • written 5.0 years ago by ▴ 40
3
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4
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1.3k
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger design matrix de
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
3
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6
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2.6k
views
Limma design/contrast correct?
limma microarray design paired mixed model
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
3
votes
6
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830
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 10 months ago by 50k • written 11 months ago by ▴ 10
3
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6
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978
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
16 months ago mohammedtoufiq91 ▴ 10
3
votes
13
replies
2.2k
views
Design and independent filtering of patient RNA-seq data
differential gene expression deseq2 design independent filtering limma
updated 8.9 years ago by 65k • written 8.9 years ago by ▴ 90
3
votes
9
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1.7k
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Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
13 months ago • updated 12 months ago mohammedtoufiq91 ▴ 10
3
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4
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2.0k
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
7
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1.8k
views
DESeq2 design formula: how to account for twin data (MZ and DZ)?
DESeq2 twins design formula RNA-seq
6.5 years ago Simone • 0
3
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5
replies
1.4k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 40
2
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2
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245
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago Sabiha ▴ 20
2
votes
8
replies
2.4k
views
DESeq design question
deseq2 design
9.4 years ago • updated 9.1 years ago sunkid • 0
2
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3
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2.9k
views
Help with DESeq2 Multiple Factor Design
deseq2 design multiple factor design
updated 9.1 years ago by ▴ 610 • written 9.1 years ago by • 0
2
votes
4
replies
1.1k
views
design microarrays limma
limma statistical power design variability microarray
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
2
votes
4
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915
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Limma model for paired and pool together
limma design rnaseq
updated 6.0 years ago by ★ 7.9k • written 6.0 years ago by ▴ 360
2
votes
1
reply
1.2k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 4.3 years ago by ▴ 50 • written 4.3 years ago by ★ 1.5k
2
votes
7
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2.0k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 3.9 years ago by 50k • written 3.9 years ago by • 0
2
votes
8
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4.2k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
3.7 years ago Pietro ▴ 40
2
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5
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1.1k
views
Picking the right design formula
deseq2 design experiment
3.6 years ago donnenfieldjonah • 0
2
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3
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826
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EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 3.5 years ago by 65k • written 3.5 years ago by • 0
2
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3
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7.4k
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DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by ▴ 30
2
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5
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3.2k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 18 months ago by 41k • written 2.8 years ago by • 0
2
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3
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1.3k
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Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
2
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2
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1.5k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 23 months ago by 50k • written 23 months ago by ▴ 10
2
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3
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1.2k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 2.9 years ago by 50k • written 2.9 years ago by • 0
2
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2
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269
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
11 weeks ago SamGG ▴ 350
2
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3
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278
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
2
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2
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818
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
14 months ago Hatchet • 0
2
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3
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1.3k
views
how to set design for 2-dye Agilent array experiment with common reference group?
limma 2-dye agilent common reference design
updated 8.4 years ago by 65k • written 8.4 years ago by ★ 3.9k
1
vote
2
replies
781
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
16 months ago mohammedtoufiq91 ▴ 10
1
vote
2
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745
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
16 months ago mohammedtoufiq91 ▴ 10
1
vote
1
reply
25k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 4.3 years ago by 41k • written 4.3 years ago by ★ 1.5k
1
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1
reply
790
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 2.4 years ago by 41k • written 2.4 years ago by • 0
1
vote
4
replies
806
views
Help with Deseq2 design
deseq2 design multifactor
updated 4.3 years ago by 41k • written 4.3 years ago by • 0
1
vote
6
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1.4k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 4.4 years ago by 65k • written 4.4 years ago by ▴ 730
1
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8
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1.5k
views
design versus interaction term similarities and/or differences?
deseq2 ANOVA design interaction term
updated 6.2 years ago by 41k • written 6.2 years ago by • 0
1
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2
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1.6k
views
DESeq2 - Design for TCGA unpaired RNAseq data
DESeq2 design TCGA unpaired RNAseq
updated 6.3 years ago by 41k • written 6.3 years ago by ▴ 10
1
vote
1
reply
937
views
Best formula to use for this experimental setup
deseq2 differential gene expression design
updated 8.8 years ago by 41k • written 8.8 years ago by • 0
1
vote
2
replies
948
views
DESeq2 design with different cell lines and disease status
deseq2 design
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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