Showing : DESIGN • reset
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edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 4 months ago by 52k • written 4 months ago by • 0
3
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3
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737
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 7 months ago by 52k • written 7 months ago by • 0
0
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6
replies
736
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 7 months ago by ★ 1.4k • written 7 months ago by ▴ 130
2
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3
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619
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 9 months ago by 52k • written 9 months ago by • 0
2
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2
replies
539
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 months ago Sabiha ▴ 20
2
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2
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516
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Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
10 months ago SamGG ▴ 360
3
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6
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1.2k
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 19 months ago by 52k • written 19 months ago by ▴ 10
3
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9
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2.6k
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Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
21 months ago mohammedtoufiq91 ▴ 10
6
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11
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1.8k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
22 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
22 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
2.0 years ago mohammedtoufiq91 ▴ 10
1
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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
2.1 years ago mohammedtoufiq91 ▴ 10
1
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2
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982
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Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
2.1 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 2.1 years ago by 43k • written 2.2 years ago by ▴ 10
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5
replies
1.3k
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 2.2 years ago by • 0 • written 2.2 years ago by • 0
2
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5
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4.0k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 2.2 years ago by 43k • written 3.5 years ago by • 0
0
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1
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751
views
Design Matrix Singularity Error
DES DESIGN
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
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2
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876
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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
2.1k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 2.6 years ago by 52k • written 2.6 years ago by ▴ 10
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4
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1.2k
views
DESeq2 pseudotime series design?
DESeq2 design
2.8 years ago jordi.planells • 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 3.0 years ago by 43k • written 3.0 years ago by • 0
0
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1
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954
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
1
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1
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961
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 3.1 years ago by 43k • written 3.1 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
3.1 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 3.1 years ago by ★ 1.4k • written 3.1 years ago by • 0
0
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1
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779
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
replies
1.2k
views
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
views
Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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1
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2.1k
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
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1.2k
views
Subject paired DESeq2 design
DESeq2 paired design
updated 3.4 years ago by 43k • written 3.4 years ago by ▴ 10
0
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1
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860
views
[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 3.4 years ago by 43k • written 3.5 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 3.6 years ago by 52k • written 3.6 years ago by • 0
2
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3
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9.6k
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DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by ▴ 30
0
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1
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892
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DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 4.2 years ago by 43k • written 4.2 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 4.2 years ago by 67k • written 4.2 years ago by • 0
0
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5
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2.1k
views
DESeq2 issue with hierarchical clustering
deseq2 design
updated 4.3 years ago by ★ 4.0k • written 4.3 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
4.3 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
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8
replies
5.1k
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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992
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 4.5 years ago by 52k • written 4.5 years ago by • 0
2
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7
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2.4k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 4.5 years ago by 52k • written 4.5 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 4.9 years ago by ★ 13k • written 4.9 years ago by • 0
0
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10
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3.1k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 4.9 years ago by ★ 1.4k • written 4.9 years ago by • 0
1
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4
replies
1.0k
views
Help with Deseq2 design
deseq2 design multifactor
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
1
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1
reply
27k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 4.9 years ago by 43k • written 4.9 years ago by ★ 1.5k
0
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2
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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
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1
reply
1.6k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 5.0 years ago by ▴ 50 • written 5.0 years ago by ★ 1.5k
1
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8
replies
9.0k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 4.0 years ago by 43k • written 5.1 years ago by • 0
1
vote
6
replies
1.8k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 5.1 years ago by 67k • written 5.1 years ago by ▴ 760
50 results • Page 1 of 1
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Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Comment: Packages don't update, but no error or warning is thrown by neighsanlo • 0
This is useful information.
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by freemanmclaughlin9969289 • 0
Tools such as Pathway Analysis with Deweighting of Overlapping Genes ([block blast][1]) or Gene Set Enrichment Analysis for Single Cell RNA…
Comment: How to get around the warning message: mzR has been built against a different Rc by Nan • 0
Hello, I was wondering if you were able to resolve this issue? I've recently encountered a similar problem and would like to ask for your a…
Votes
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
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