Showing : design • reset
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518
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edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 8 months ago by 52k • written 8 months ago by • 0
3
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3
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955
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 11 months ago by 52k • written 11 months ago by • 0
0
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6
replies
918
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 11 months ago by ★ 1.4k • written 11 months ago by ▴ 130
2
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3
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820
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 13 months ago by 52k • written 13 months ago by • 0
2
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2
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644
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
13 months ago Sabiha ▴ 20
2
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2
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614
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Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
14 months ago SamGG ▴ 360
3
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6
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1.3k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 23 months ago by 52k • written 23 months ago by ▴ 10
3
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9
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2.9k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
2.1 years ago mohammedtoufiq91 ▴ 10
6
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11
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2.0k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.2 years ago mohammedtoufiq91 ▴ 10
2
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2
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1.2k
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Updating DESeq2 object's design with sva output
DESeq2 design sva
2.2 years ago Hatchet • 0
3
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6
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1.6k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
2.4 years ago mohammedtoufiq91 ▴ 10
1
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2
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1.1k
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
2.4 years ago mohammedtoufiq91 ▴ 10
1
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2
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1.1k
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
2.4 years ago mohammedtoufiq91 ▴ 10
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13
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3.1k
views
DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 2.4 years ago by 43k • written 2.5 years ago by ▴ 10
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5
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1.5k
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 2.5 years ago by • 0 • written 2.5 years ago by • 0
2
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5
replies
4.3k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 2.5 years ago by 43k • written 3.8 years ago by • 0
0
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1
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836
views
Design Matrix Singularity Error
DES DESIGN
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
0
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2
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941
views
Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
2
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2
replies
2.4k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 2.9 years ago by 52k • written 2.9 years ago by ▴ 10
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4
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1.3k
views
DESeq2 pseudotime series design?
DESeq2 design
3.1 years ago jordi.planells • 0
0
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2
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1.1k
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DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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1
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1.0k
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
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1
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1.0k
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
1
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2
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1.4k
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
3.4 years ago Barista • 0
0
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2
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1.4k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 3.5 years ago by ★ 1.4k • written 3.5 years ago by • 0
0
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1
reply
845
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
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2
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1.4k
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Design formula in DESeq2
model BatchEffect hidden Design DESeq2
3.5 years ago m.glymenaki • 0
2
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3
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1.8k
views
Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
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1
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2.4k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
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1
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1.2k
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Subject paired DESeq2 design
DESeq2 paired design
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 10
0
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1
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927
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[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 3.7 years ago by 43k • written 3.8 years ago by • 0
2
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3
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1.6k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.9 years ago by 52k • written 3.9 years ago by • 0
2
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3
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11k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by ▴ 30
0
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1
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954
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 50
2
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3
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1.1k
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
0
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5
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2.3k
views
DESeq2 issue with hierarchical clustering
deseq2 design
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by • 0
2
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5
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1.5k
views
Picking the right design formula
deseq2 design experiment
4.6 years ago donnenfieldjonah • 0
4
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5
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3.8k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
2
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8
replies
5.5k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
4.7 years ago Pietro ▴ 40
4
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7
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1.6k
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 4.8 years ago by 52k • written 4.8 years ago by • 0
0
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1
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1.1k
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 4.9 years ago by 52k • written 4.9 years ago by • 0
2
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7
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2.7k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 4.9 years ago by 52k • written 4.9 years ago by • 0
6
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6
replies
1.6k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 5.2 years ago by ★ 13k • written 5.2 years ago by • 0
0
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10
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3.6k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 5.2 years ago by ★ 1.4k • written 5.2 years ago by • 0
1
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4
replies
1.1k
views
Help with Deseq2 design
deseq2 design multifactor
updated 5.2 years ago by 43k • written 5.2 years ago by • 0
1
vote
1
reply
28k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ★ 1.5k
0
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2
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1.5k
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
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1
reply
1.7k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 5.3 years ago by ▴ 60 • written 5.3 years ago by ★ 1.5k
1
vote
8
replies
9.9k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 4.3 years ago by 43k • written 5.4 years ago by • 0
1
vote
6
replies
2.1k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 5.4 years ago by 68k • written 5.4 years ago by ▴ 760
50 results • Page 1 of 1
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Replies
Comment: RNA Seq using Lrt by Rob • 0
So if I have understood what you have said : If i want to see if Day (time) has an effect / is being tested - then the reduced model should…
Comment: How to convert transcript counts to gene counts in R? by ben • 0
Simply summing transcripts by gene is sufficient for use with DESeq2. [sprunki clicker][1] [1]: https://sprunkiclicker.com/
Answer: EuroBioC2024 abstract submission is open! by Ali • 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets by Gordon Smyth 52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Votes
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
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