Showing : Design • reset
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edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 5 months ago by 52k • written 5 months ago by • 0
3
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3
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797
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 8 months ago by 52k • written 8 months ago by • 0
0
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6
replies
775
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 9 months ago by ★ 1.4k • written 9 months ago by ▴ 130
2
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3
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667
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 10 months ago by 52k • written 10 months ago by • 0
2
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2
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571
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
10 months ago Sabiha ▴ 20
2
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2
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541
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Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
11 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 20 months ago by 52k • written 20 months ago by ▴ 10
3
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9
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2.6k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
22 months ago mohammedtoufiq91 ▴ 10
6
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11
replies
1.9k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
23 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
23 months 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
2.1 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
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999
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
2.2 years ago mohammedtoufiq91 ▴ 10
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13
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2.8k
views
DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 2.2 years ago by 43k • written 2.3 years ago by ▴ 10
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5
replies
1.4k
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 2.3 years ago by • 0 • written 2.3 years ago by • 0
2
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5
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4.1k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 2.3 years ago by 43k • written 3.6 years ago by • 0
0
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1
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767
views
Design Matrix Singularity Error
DES DESIGN
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
0
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2
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886
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Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 2.6 years ago by 43k • written 2.6 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 2.7 years ago by 52k • written 2.7 years ago by ▴ 10
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4
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1.2k
views
DESeq2 pseudotime series design?
DESeq2 design
2.9 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 3.1 years ago by 43k • written 3.1 years ago by • 0
0
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1
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976
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
977
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
1
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2
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1.3k
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
3.2 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 3.2 years ago by ★ 1.4k • written 3.2 years ago by • 0
0
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1
reply
790
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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2
replies
1.3k
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
3.2 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 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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1
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2.2k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
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1
reply
1.2k
views
Subject paired DESeq2 design
DESeq2 paired design
updated 3.5 years ago by 43k • written 3.5 years ago by ▴ 10
0
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1
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879
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[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 3.5 years ago by 43k • written 3.6 years ago by • 0
2
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3
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1.5k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.7 years ago by 52k • written 3.7 years ago by • 0
2
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3
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9.8k
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DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by ▴ 30
0
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1
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903
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 4.3 years ago by 43k • written 4.3 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 4.3 years ago by 67k • written 4.3 years ago by • 0
0
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5
replies
2.1k
views
DESeq2 issue with hierarchical clustering
deseq2 design
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
2
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5
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1.4k
views
Picking the right design formula
deseq2 design experiment
4.4 years ago donnenfieldjonah • 0
4
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5
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3.5k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 4.4 years ago by 67k • written 4.4 years ago by • 0
2
votes
8
replies
5.2k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
4.4 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 4.5 years ago by 52k • written 4.5 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 4.6 years ago by 52k • written 4.6 years ago by • 0
2
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7
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2.5k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 4.6 years ago by 52k • written 4.6 years ago by • 0
6
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6
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1.5k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 5.0 years ago by ★ 13k • written 5.0 years ago by • 0
0
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10
replies
3.2k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 5.0 years ago by ★ 1.4k • written 5.0 years ago by • 0
1
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4
replies
1.1k
views
Help with Deseq2 design
deseq2 design multifactor
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
1
vote
1
reply
27k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 5.0 years ago by 43k • written 5.0 years ago by ★ 1.5k
0
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2
replies
1.3k
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
2
votes
1
reply
1.6k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 5.1 years ago by ▴ 50 • written 5.1 years ago by ★ 1.5k
1
vote
8
replies
9.2k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 4.1 years ago by 43k • written 5.2 years ago by • 0
1
vote
6
replies
1.9k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 5.2 years ago by 67k • written 5.2 years ago by ▴ 760
50 results • Page 1 of 1
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Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
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Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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