Showing : DESIGN • reset
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edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 14 months ago by 53k • written 14 months ago by • 0
3
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3
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1.1k
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 16 months ago by 53k • written 16 months ago by • 0
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6
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1.1k
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 17 months ago by ★ 1.4k • written 17 months ago by ▴ 130
2
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3
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1.0k
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 18 months ago by 53k • written 18 months ago by • 0
2
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2
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771
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
19 months ago Sabiha ▴ 20
2
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2
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716
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Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
20 months ago SamGG ▴ 360
3
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6
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1.5k
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.3 years ago by 53k • written 2.4 years ago by ▴ 10
3
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9
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3.3k
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Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
2.5 years ago mohammedtoufiq91 ▴ 10
6
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11
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2.3k
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Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.6 years ago mohammedtoufiq91 ▴ 10
2
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2
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1.3k
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Updating DESeq2 object's design with sva output
DESeq2 design sva
2.6 years ago Hatchet • 0
3
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6
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1.8k
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
2.8 years ago mohammedtoufiq91 ▴ 10
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2
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1.2k
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
2.8 years ago mohammedtoufiq91 ▴ 10
1
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2
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1.2k
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Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
2.8 years ago mohammedtoufiq91 ▴ 10
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13
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3.5k
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DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 2.9 years ago by 43k • written 3.0 years ago by ▴ 10
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5
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1.7k
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Inquiry about suitable package for proteomics study design
Proteomics design
updated 3.0 years ago by • 0 • written 3.0 years ago by • 0
2
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5
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4.5k
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DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 3.0 years ago by 43k • written 4.3 years ago by • 0
0
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1
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945
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Design Matrix Singularity Error
DES DESIGN
updated 3.0 years ago by 43k • written 3.1 years ago by • 0
0
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2
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1.0k
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Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
2
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2
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2.6k
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Handling NA values in limma's voom design matrix
limma voom design NAs
updated 3.4 years ago by 53k • written 3.4 years ago by ▴ 10
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4
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1.6k
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DESeq2 pseudotime series design?
DESeq2 design
3.6 years ago jordi.planells • 0
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2
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1.2k
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DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
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1
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1.1k
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Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
1
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1
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1.1k
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Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
1
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2
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1.5k
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
3.9 years ago Barista • 0
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2
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1.5k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 3.9 years ago by ★ 1.4k • written 3.9 years ago by • 0
0
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1
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917
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Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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2
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1.5k
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Design formula in DESeq2
model BatchEffect hidden Design DESeq2
3.9 years ago m.glymenaki • 0
2
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3
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2.0k
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Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
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1
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2.6k
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DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
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1
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1.4k
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Subject paired DESeq2 design
DESeq2 paired design
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 10
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1
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1.0k
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[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
2
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3
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1.8k
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Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 4.4 years ago by 53k • written 4.4 years ago by • 0
2
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3
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11k
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DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 4.7 years ago by ★ 4.0k • written 4.8 years ago by ▴ 30
0
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1
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1.0k
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 50
2
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3
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1.3k
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EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
0
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5
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2.5k
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DESeq2 issue with hierarchical clustering
deseq2 design
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by • 0
2
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5
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1.6k
views
Picking the right design formula
deseq2 design experiment
5.1 years ago donnenfieldjonah • 0
4
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5
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4.1k
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How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
2
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8
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5.9k
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Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
5.1 years ago Pietro ▴ 40
4
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7
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1.7k
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Genes upregulated in one condition vs each of the other conditions
edger design
updated 5.2 years ago by 53k • written 5.2 years ago by • 0
0
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1
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1.2k
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 5.3 years ago by 53k • written 5.3 years ago by • 0
2
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7
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2.9k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 5.3 years ago by 53k • written 5.3 years ago by • 0
6
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6
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1.9k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 5.6 years ago by ★ 13k • written 5.6 years ago by • 0
0
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10
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4.0k
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DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 5.7 years ago by ★ 1.4k • written 5.7 years ago by • 0
1
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4
replies
1.2k
views
Help with Deseq2 design
deseq2 design multifactor
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
1
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1
reply
28k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 5.7 years ago by 43k • written 5.7 years ago by ★ 1.5k
0
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2
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1.6k
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Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
2
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1
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1.8k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 5.7 years ago by ▴ 60 • written 5.7 years ago by ★ 1.5k
1
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10
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11k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 10 weeks ago by 43k • written 5.9 years ago by • 0
1
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6
replies
2.2k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 760
93 results • Page 1 of 2
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Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 4.9k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 4.9k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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