Showing : DESIGN • reset
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edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 3 months ago by 51k • written 3 months ago by • 0
3
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3
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678
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 6 months ago by 51k • written 6 months ago by • 0
0
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6
replies
688
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 6 months ago by ★ 1.4k • written 6 months ago by ▴ 130
2
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3
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570
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 8 months ago by 51k • written 8 months ago by • 0
2
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2
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507
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 months ago Sabiha ▴ 20
2
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2
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494
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Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
9 months ago SamGG ▴ 350
3
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6
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1.1k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 18 months ago by 51k • written 18 months ago by ▴ 10
3
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9
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2.5k
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Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
20 months ago mohammedtoufiq91 ▴ 10
6
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11
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1.8k
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Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
21 months ago mohammedtoufiq91 ▴ 10
2
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2
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1.1k
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Updating DESeq2 object's design with sva output
DESeq2 design sva
21 months ago Hatchet • 0
3
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6
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1.4k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
23 months ago mohammedtoufiq91 ▴ 10
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2
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1.0k
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Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
24 months ago mohammedtoufiq91 ▴ 10
1
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2
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966
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Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
24 months ago mohammedtoufiq91 ▴ 10
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13
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2.7k
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DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 2.0 years ago by 43k • written 2.1 years ago by ▴ 10
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5
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1.3k
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Inquiry about suitable package for proteomics study design
Proteomics design
updated 2.1 years ago by • 0 • written 2.1 years ago by • 0
2
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5
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3.9k
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DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 2.1 years ago by 43k • written 3.4 years ago by • 0
0
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1
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727
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Design Matrix Singularity Error
DES DESIGN
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
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2
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864
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Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
2
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2
replies
2.0k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 2.5 years ago by 51k • written 2.5 years ago by ▴ 10
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4
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1.2k
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DESeq2 pseudotime series design?
DESeq2 design
2.7 years ago jordi.planells • 0
0
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2
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1.0k
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DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
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1
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920
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
1
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1
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949
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Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
1
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2
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1.2k
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
3.0 years ago Barista • 0
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2
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1.2k
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DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by • 0
0
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1
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764
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
0
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2
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1.2k
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Design formula in DESeq2
model BatchEffect hidden Design DESeq2
3.1 years ago m.glymenaki • 0
2
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3
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1.6k
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Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
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1
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2.1k
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DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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1
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1.1k
views
Subject paired DESeq2 design
DESeq2 paired design
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
0
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1
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839
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[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 3.3 years ago by 43k • written 3.4 years ago by • 0
2
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3
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1.4k
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Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.5 years ago by 51k • written 3.5 years ago by • 0
2
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3
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9.3k
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DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 3.9 years ago by ★ 4.0k • written 3.9 years ago by ▴ 30
0
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1
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877
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DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 50
2
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3
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1.0k
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 4.1 years ago by 67k • written 4.1 years ago by • 0
0
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5
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2.1k
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DESeq2 issue with hierarchical clustering
deseq2 design
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
2
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5
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1.4k
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Picking the right design formula
deseq2 design experiment
4.2 years ago donnenfieldjonah • 0
4
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5
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3.4k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 4.3 years ago by 67k • written 4.3 years ago by • 0
2
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8
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5.0k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
4.3 years ago Pietro ▴ 40
4
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7
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1.4k
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 4.4 years ago by 51k • written 4.4 years ago by • 0
0
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1
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977
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Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 4.4 years ago by 51k • written 4.4 years ago by • 0
2
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7
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2.4k
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Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 4.5 years ago by 51k • written 4.5 years ago by • 0
6
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6
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1.4k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 4.8 years ago by ★ 13k • written 4.8 years ago by • 0
0
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10
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3.0k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 4.8 years ago by ★ 1.4k • written 4.8 years ago by • 0
1
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4
replies
1.0k
views
Help with Deseq2 design
deseq2 design multifactor
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
1
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1
reply
27k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 4.8 years ago by 43k • written 4.9 years ago by ★ 1.5k
0
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2
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1.3k
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Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
2
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1
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1.5k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 4.9 years ago by ▴ 50 • written 4.9 years ago by ★ 1.5k
1
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8
replies
8.7k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 3.9 years ago by 43k • written 5.0 years ago by • 0
1
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6
replies
1.8k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 5.0 years ago by 67k • written 5.0 years ago by ▴ 760
50 results • Page 1 of 1
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Replies
Answer: Deseq2 res Function by Michael Love 43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Votes
Comment: Is it recommended to analyze different tissues together when using edgeR
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
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