Showing : Design • reset
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How to create design matrix for trait association to modules in WGCNA analysis in R
modules wgcna edgeR limma design
15 hours ago • updated 3 hours ago mohammedtoufiq91 ▴ 10
3
votes
9
replies
446
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
9 weeks ago • updated 8 weeks ago mohammedtoufiq91 ▴ 10
6
votes
11
replies
557
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
3 months ago mohammedtoufiq91 ▴ 10
2
votes
2
replies
200
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
3 months ago Hatchet • 0
3
votes
6
replies
410
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
5 months ago mohammedtoufiq91 ▴ 10
1
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2
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287
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
5 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
354
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
5 months ago mohammedtoufiq91 ▴ 10
0
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13
replies
925
views
DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 6 months ago by 40k • written 7 months ago by ▴ 10
0
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5
replies
453
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 7 months ago by • 0 • written 7 months ago by • 0
2
votes
5
replies
1.9k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 7 months ago by 40k • written 23 months ago by • 0
0
votes
1
reply
270
views
Design Matrix Singularity Error
DES DESIGN
updated 8 months ago by 40k • written 8 months ago by • 0
0
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2
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364
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Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 11 months ago by 40k • written 11 months ago by • 0
2
votes
2
replies
628
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 12 months ago by 47k • written 12 months ago by ▴ 10
0
votes
4
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586
views
DESeq2 pseudotime series design?
DESeq2 design
15 months ago • updated 14 months ago jordi.planells • 0
0
votes
2
replies
510
views
DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 17 months ago by 40k • written 17 months ago by • 0
0
votes
1
reply
450
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 18 months ago by 40k • written 18 months ago by • 0
1
vote
1
reply
498
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 18 months ago by 40k • written 18 months ago by • 0
1
vote
2
replies
615
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
18 months ago Barista • 0
0
votes
2
replies
666
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 18 months ago by ★ 1.2k • written 18 months ago by • 0
0
votes
1
reply
348
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 19 months ago by 40k • written 19 months ago by • 0
0
votes
2
replies
522
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
19 months ago m.glymenaki • 0
2
votes
3
replies
817
views
Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 19 months ago by 40k • written 19 months ago by • 0
0
votes
1
reply
1.1k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 21 months ago by 40k • written 21 months ago by • 0
0
votes
1
reply
555
views
Subject paired DESeq2 design
DESeq2 paired design
updated 22 months ago by 40k • written 22 months ago by ▴ 10
0
votes
1
reply
463
views
[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 22 months ago by 40k • written 23 months ago by • 0
2
votes
3
replies
778
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 24 months ago by 47k • written 2.0 years ago by • 0
2
votes
3
replies
4.5k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 2.4 years ago by 3.8k • written 2.4 years ago by ▴ 20
0
votes
1
reply
436
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 2.6 years ago by 40k • written 2.6 years ago by ▴ 20
2
votes
3
replies
549
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 2.6 years ago by 62k • written 2.6 years ago by • 0
0
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5
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884
views
DESeq2 issue with hierarchical clustering
deseq2 design
updated 2.7 years ago by 3.8k • written 2.7 years ago by • 0
2
votes
5
replies
694
views
Picking the right design formula
deseq2 design experiment
2.7 years ago donnenfieldjonah • 0
4
votes
5
replies
2.0k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 2.8 years ago by 62k • written 2.8 years ago by • 0
2
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8
replies
2.9k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
2.8 years ago Pietro ▴ 40
4
votes
7
replies
625
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 2.9 years ago by 47k • written 2.9 years ago by • 0
0
votes
1
reply
484
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 3.0 years ago by 47k • written 3.0 years ago by • 0
2
votes
7
replies
1.2k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 3.0 years ago by 47k • written 3.0 years ago by • 0
6
votes
6
replies
732
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 3.3 years ago by 13k • written 3.3 years ago by • 0
0
votes
10
replies
1.4k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 3.3 years ago by ★ 1.2k • written 3.3 years ago by • 0
1
vote
4
replies
532
views
Help with Deseq2 design
deseq2 design multifactor
updated 3.3 years ago by 40k • written 3.3 years ago by • 0
1
vote
1
reply
22k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 3.4 years ago by 40k • written 3.4 years ago by ★ 1.5k
0
votes
2
replies
565
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 3.4 years ago by 40k • written 3.4 years ago by • 0
2
votes
1
reply
647
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 3.4 years ago by ▴ 50 • written 3.4 years ago by ★ 1.5k
1
vote
8
replies
4.8k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 2.4 years ago by 40k • written 3.5 years ago by • 0
1
vote
6
replies
960
views
Relations between average expression and fold change
design AveExpr comparisons
updated 3.5 years ago by 62k • written 3.5 years ago by ▴ 710
0
votes
1
reply
1.1k
views
DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2 comparison design paired treatment
updated 3.5 years ago by ★ 1.2k • written 3.5 years ago by • 0
0
votes
4
replies
1.3k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
3.6 years ago luciest.rodriguez • 0
0
votes
2
replies
553
views
different designs for finding DEG by limma
limma DEG design
3.7 years ago amin.ghareyazi • 0
0
votes
8
replies
1.2k
views
Two controls in RNAseq formula for DESeq2
deseq2 formula controls design
updated 3.8 years ago by 40k • written 3.8 years ago by • 0
0
votes
3
replies
558
views
Analysis strategy - possible to use naive control group as t=0 for two treatment groups?
Deseq2 design time course basal group
updated 3.9 years ago by 40k • written 3.9 years ago by • 0
4
votes
18
replies
21k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 3.9 years ago by • 0 • written 8.6 years ago by ▴ 100
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Comment: BiocGenerics binary is outdated for macOS ARM by jennifer.wokaty ▴ 60
Thanks, Mike, for posting about this and thanks to Lori for noticing the lock. I removed it and RProtoBufLib passes R CMD check. Unfortunat…
Comment: BiocGenerics binary is outdated for macOS ARM by Michael Steinbaugh ▴ 90
Ah thanks for the update. Yeah I see that the flowClust release is the culprit: https://www.bioconductor.org/packages/release/bioc/html/flo…
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are you talking specifically on the support site or elsewhere also?
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flowCore: using read.FCS with which.lines is not time efficient?
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