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
votes
3
replies
804
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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
781
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
votes
3
replies
676
views
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
replies
573
views
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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542
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Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
12 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
replies
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
replies
1.1k
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Updating DESeq2 object's design with sva output
DESeq2 design sva
24 months ago • updated 23 months ago Hatchet • 0
3
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6
replies
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
replies
1000
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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2.9k
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
replies
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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768
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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888
views
Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 2.6 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 2.7 years ago by 52k • written 2.7 years ago by ▴ 10
0
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4
replies
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
views
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
reply
979
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
978
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
791
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
3.3 years ago • updated 3.2 years ago m.glymenaki • 0
2
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3
replies
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 3.5 years ago by 43k • written 3.5 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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880
views
[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
views
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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904
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
2.2k
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
replies
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 4.5 years ago by 67k • written 4.5 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
4.5 years ago Pietro ▴ 40
4
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7
replies
1.4k
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 4.6 years ago by 52k • written 4.6 years ago by • 0
2
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7
replies
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
replies
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
vote
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 5.1 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 5.1 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
Recent ...
Replies
Comment: Unused arguments error without used arguments in GSVA? by 1sunmic2 • 0
It was due to the comma. Thank you!
Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.1k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA by User3088 • 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Votes
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
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Teacher to Axel Klenk ★ 1.1k
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Popular Question to Gordon Smyth 52k
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Popular Question to Maria Doyle ▴ 100
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