Showing : design • reset
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edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 6 months ago by 52k • written 6 months ago by • 0
3
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3
replies
861
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 9 months ago by 52k • written 9 months ago by • 0
0
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6
replies
837
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 10 months ago by ★ 1.4k • written 10 months ago by ▴ 130
2
votes
3
replies
754
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 11 months ago by 52k • written 11 months ago by • 0
2
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2
replies
605
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
11 months ago Sabiha ▴ 20
2
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2
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573
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Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
13 months ago SamGG ▴ 360
3
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6
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1.2k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 21 months ago by 52k • written 21 months ago by ▴ 10
3
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9
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2.7k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
23 months ago mohammedtoufiq91 ▴ 10
6
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11
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1.9k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.1 years ago • updated 2.0 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
2.1 years ago Hatchet • 0
3
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6
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1.5k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
2.2 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
2.2 years ago mohammedtoufiq91 ▴ 10
1
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2
replies
1.0k
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
2.3 years ago mohammedtoufiq91 ▴ 10
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13
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2.9k
views
DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 2.3 years ago by 43k • written 2.4 years ago by ▴ 10
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5
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1.4k
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 2.4 years ago by • 0 • written 2.4 years ago by • 0
2
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5
replies
4.2k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 2.4 years ago by 43k • written 3.7 years ago by • 0
0
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1
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797
views
Design Matrix Singularity Error
DES DESIGN
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
0
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2
replies
911
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Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
2
votes
2
replies
2.2k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 2.8 years ago by 52k • written 2.8 years ago by ▴ 10
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4
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1.3k
views
DESeq2 pseudotime series design?
DESeq2 design
3.0 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 3.2 years ago by 43k • written 3.2 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 3.2 years ago by 43k • written 3.2 years ago by • 0
1
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1
reply
999
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
1
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2
replies
1.3k
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
3.3 years ago Barista • 0
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2
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1.3k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by • 0
0
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1
reply
818
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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2
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1.3k
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
3.3 years ago m.glymenaki • 0
2
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3
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1.7k
views
Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
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1
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2.3k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 3.5 years ago by 43k • written 3.5 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 3.6 years ago by 43k • written 3.6 years ago by ▴ 10
0
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1
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898
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[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 3.6 years ago by 43k • written 3.7 years ago by • 0
2
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3
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1.5k
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Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.8 years ago by 52k • written 3.8 years ago by • 0
2
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3
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10k
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DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by ▴ 30
0
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1
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927
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 50
2
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3
replies
1.1k
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 4.4 years ago by 68k • written 4.4 years ago by • 0
0
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5
replies
2.2k
views
DESeq2 issue with hierarchical clustering
deseq2 design
updated 4.5 years ago by ★ 4.0k • written 4.5 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
4.5 years ago donnenfieldjonah • 0
4
votes
5
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3.6k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
2
votes
8
replies
5.3k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
4.5 years ago Pietro ▴ 40
4
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7
replies
1.5k
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 4.6 years ago by 52k • written 4.6 years ago by • 0
0
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1
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1.0k
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 4.7 years ago by 52k • written 4.7 years ago by • 0
2
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7
replies
2.6k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 4.7 years ago by 52k • written 4.7 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 5.1 years ago by ★ 13k • written 5.1 years ago by • 0
0
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10
replies
3.3k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 5.1 years ago by ★ 1.4k • written 5.1 years ago by • 0
1
vote
4
replies
1.1k
views
Help with Deseq2 design
deseq2 design multifactor
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
1
vote
1
reply
28k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 5.1 years ago by 43k • written 5.1 years ago by ★ 1.5k
0
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2
replies
1.4k
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
2
votes
1
reply
1.6k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 5.2 years ago by ▴ 60 • written 5.2 years ago by ★ 1.5k
1
vote
8
replies
9.5k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 4.2 years ago by 43k • written 5.3 years ago by • 0
1
vote
6
replies
2.0k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 760
50 results • Page 1 of 1
Recent ...
Replies
Answer: myvariant error by James W. MacDonald 68k
You don't show anything about the data you are annotating, so it's hard to say what the problem might be. Does the example data work for yo…
Answer: Conumee2 - CNV.summaryplot() by James W. MacDonald 68k
There doesn't appear to be a function called `CNV.summaryplot` in `conumee`. What package does that function come from?
Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840
Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Votes
A: What is the "linear model" part used for in Limma?
Comment: Use of limma R package with targeted proteomics for DE analysis
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
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