Showing : DESIGN • reset
3
votes
4
replies
148
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Question about the filterByExpr function inputs in edgeR
RNASeq filter design edgeR model.matrix
1 day ago • updated 15 hours ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
852
views
edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 17 months ago by 53k • written 17 months ago by • 0
3
votes
3
replies
1.2k
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
6
replies
1.2k
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 20 months ago by ★ 1.4k • written 20 months ago by ▴ 130
2
votes
3
replies
1.1k
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 22 months ago by 53k • written 22 months ago by • 0
2
votes
2
replies
900
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
22 months ago Sabiha ▴ 20
2
votes
2
replies
815
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
23 months ago SamGG ▴ 360
3
votes
6
replies
1.6k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.6 years ago by 53k • written 2.6 years ago by ▴ 10
3
votes
9
replies
3.6k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
2.8 years ago mohammedtoufiq91 ▴ 10
6
votes
11
replies
2.5k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.9 years ago mohammedtoufiq91 ▴ 10
2
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2
replies
1.4k
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
2.9 years ago Hatchet • 0
3
votes
6
replies
1.9k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
3.1 years ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
1.3k
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
3.1 years ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
1.3k
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
3.1 years ago mohammedtoufiq91 ▴ 10
0
votes
13
replies
3.7k
views
DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 3.2 years ago by 43k • written 3.3 years ago by ▴ 10
0
votes
5
replies
1.8k
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 3.2 years ago by • 0 • written 3.2 years ago by • 0
2
votes
5
replies
4.7k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 3.2 years ago by 43k • written 4.6 years ago by • 0
0
votes
1
reply
1.0k
views
Design Matrix Singularity Error
DES DESIGN
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
votes
2
replies
1.1k
views
Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
2
votes
2
replies
2.8k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 10
0
votes
4
replies
1.7k
views
DESeq2 pseudotime series design?
DESeq2 design
3.9 years ago jordi.planells • 0
0
votes
2
replies
1.3k
views
DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
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1
reply
1.2k
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
1
vote
1
reply
1.2k
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
1
vote
2
replies
1.7k
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
4.2 years ago Barista • 0
0
votes
2
replies
1.6k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 4.2 years ago by ★ 1.4k • written 4.2 years ago by • 0
0
votes
1
reply
983
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
0
votes
2
replies
1.7k
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
4.2 years ago m.glymenaki • 0
2
votes
3
replies
2.2k
views
Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
0
votes
1
reply
2.8k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
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1
reply
1.5k
views
Subject paired DESeq2 design
DESeq2 paired design
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 10
0
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1
reply
1.1k
views
[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
2
votes
3
replies
1.9k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 4.6 years ago by 53k • written 4.6 years ago by • 0
2
votes
3
replies
12k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 5.0 years ago by ★ 4.0k • written 5.0 years ago by ▴ 30
0
votes
1
reply
1.1k
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 50
2
votes
3
replies
1.3k
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
0
votes
5
replies
2.6k
views
DESeq2 issue with hierarchical clustering
deseq2 design
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
2
votes
5
replies
1.7k
views
Picking the right design formula
deseq2 design experiment
5.3 years ago donnenfieldjonah • 0
4
votes
5
replies
4.3k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
2
votes
8
replies
6.1k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
5.4 years ago Pietro ▴ 40
4
votes
7
replies
1.9k
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 5.5 years ago by 53k • written 5.5 years ago by • 0
0
votes
1
reply
1.3k
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
2
votes
7
replies
3.1k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 5.6 years ago by 53k • written 5.6 years ago by • 0
6
votes
6
replies
2.0k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 5.9 years ago by ★ 13k • written 5.9 years ago by • 0
0
votes
10
replies
4.3k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 5.9 years ago by ★ 1.4k • written 5.9 years ago by • 0
1
vote
4
replies
1.3k
views
Help with Deseq2 design
deseq2 design multifactor
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
1
vote
1
reply
28k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ★ 1.5k
0
votes
2
replies
1.7k
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
2
votes
1
reply
1.9k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 6.0 years ago by ▴ 60 • written 6.0 years ago by ★ 1.5k
1
vote
10
replies
11k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 5 months ago by 43k • written 6.1 years ago by • 0
94 results • Page 1 of 2
Recent ...
Replies
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Votes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
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