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 17 months ago by 53k • written 17 months ago by • 0
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 19 months ago by 53k • written 19 months ago by • 0
2
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2
replies
784
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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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721
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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
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
3
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9
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3.3k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
2.6 years ago • updated 2.5 years ago mohammedtoufiq91 ▴ 10
6
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11
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2.3k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.7 years ago mohammedtoufiq91 ▴ 10
2
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2
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1.4k
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
2.7 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
1
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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
2.9 years ago mohammedtoufiq91 ▴ 10
1
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2
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1.2k
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
2.9 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
views
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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951
views
Design Matrix Singularity Error
DES DESIGN
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
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2
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1.0k
views
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 3.9 years ago by 43k • written 3.9 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 3.9 years ago by 43k • written 3.9 years ago by • 0
1
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2
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1.5k
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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
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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925
views
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
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
views
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
0
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1
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2.7k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 4.2 years ago by 43k • written 4.2 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
0
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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 4.3 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 4.8 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
views
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 5.1 years ago by ★ 4.0k • written 5.1 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
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
2
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8
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5.9k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
5.2 years ago Pietro ▴ 40
4
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7
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1.7k
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 5.2 years ago by 53k • written 5.3 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
replies
1.9k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 5.7 years ago by ★ 13k • written 5.7 years ago by • 0
0
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10
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4.0k
views
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
vote
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
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 5.8 years ago by 43k • written 5.8 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 5.8 years ago by ▴ 60 • written 5.8 years ago by ★ 1.5k
1
vote
10
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11k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 11 weeks ago by 43k • written 5.9 years ago by • 0
1
vote
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
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
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 ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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