Showing : DESIGN • reset
2
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3
replies
277
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
2
votes
2
replies
244
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago • updated 5 weeks ago Sabiha ▴ 20
2
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2
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268
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Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
11 weeks ago SamGG ▴ 350
3
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6
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828
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 10 months ago by 50k • written 11 months ago by ▴ 10
3
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9
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1.7k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
13 months ago • updated 12 months ago mohammedtoufiq91 ▴ 10
6
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11
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1.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
14 months ago mohammedtoufiq91 ▴ 10
2
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2
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818
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Updating DESeq2 object's design with sva output
DESeq2 design sva
14 months ago Hatchet • 0
3
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6
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978
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
16 months ago mohammedtoufiq91 ▴ 10
1
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2
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745
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Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
16 months ago mohammedtoufiq91 ▴ 10
1
vote
2
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781
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Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
16 months ago mohammedtoufiq91 ▴ 10
0
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5
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981
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Inquiry about suitable package for proteomics study design
Proteomics design
updated 18 months ago by • 0 • written 18 months ago by • 0
0
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13
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2.1k
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DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 17 months ago by 41k • written 18 months ago by ▴ 10
0
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1
reply
556
views
Design Matrix Singularity Error
DES DESIGN
updated 19 months ago by 41k • written 19 months ago by • 0
0
votes
2
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669
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Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 22 months ago by 41k • written 22 months ago by • 0
2
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2
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1.5k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 23 months ago by 50k • written 23 months ago by ▴ 10
0
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4
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971
views
DESeq2 pseudotime series design?
DESeq2 design
2.1 years ago jordi.planells • 0
0
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2
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843
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DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
0
votes
1
reply
742
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 2.4 years ago by 41k • written 2.4 years ago by • 0
1
vote
1
reply
790
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 2.4 years ago by 41k • written 2.4 years ago by • 0
1
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2
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960
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
2.4 years ago Barista • 0
0
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2
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996
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 2.5 years ago by ★ 1.3k • written 2.5 years ago by • 0
0
votes
1
reply
609
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
0
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2
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922
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Design formula in DESeq2
model BatchEffect hidden Design DESeq2
2.5 years ago m.glymenaki • 0
2
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3
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1.3k
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Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
0
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1
reply
1.7k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
0
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1
reply
945
views
Subject paired DESeq2 design
DESeq2 paired design
updated 2.7 years ago by 41k • written 2.7 years ago by ▴ 10
0
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1
reply
688
views
[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 2.7 years ago by 41k • written 2.8 years ago by • 0
2
votes
5
replies
3.2k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 18 months ago by 41k • written 2.8 years ago by • 0
2
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3
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1.2k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 2.9 years ago by 50k • written 2.9 years ago by • 0
2
votes
3
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7.4k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by ▴ 30
0
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1
reply
747
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 3.5 years ago by 41k • written 3.5 years ago by ▴ 40
2
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3
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826
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 3.5 years ago by 65k • written 3.5 years ago by • 0
0
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5
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1.6k
views
DESeq2 issue with hierarchical clustering
deseq2 design
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
2
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5
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1.1k
views
Picking the right design formula
deseq2 design experiment
3.6 years ago donnenfieldjonah • 0
4
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5
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2.9k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 3.7 years ago by 65k • written 3.7 years ago by • 0
2
votes
8
replies
4.2k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
3.7 years ago Pietro ▴ 40
4
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7
replies
1.1k
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 3.8 years ago by 50k • written 3.8 years ago by • 0
0
votes
1
reply
792
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 3.9 years ago by 50k • written 3.9 years ago by • 0
2
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7
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2.0k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 3.9 years ago by 50k • written 3.9 years ago by • 0
6
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6
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1.2k
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Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 4.2 years ago by ★ 13k • written 4.2 years ago by • 0
0
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10
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2.4k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 4.2 years ago by ★ 1.3k • written 4.2 years ago by • 0
1
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4
replies
806
views
Help with Deseq2 design
deseq2 design multifactor
updated 4.3 years ago by 41k • written 4.3 years ago by • 0
1
vote
1
reply
25k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 4.3 years ago by 41k • written 4.3 years ago by ★ 1.5k
0
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2
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951
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 4.3 years ago by 41k • written 4.3 years ago by • 0
2
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1
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1.2k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 4.3 years ago by ▴ 50 • written 4.3 years ago by ★ 1.5k
1
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8
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7.1k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 3.3 years ago by 41k • written 4.4 years ago by • 0
1
vote
6
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1.4k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 4.4 years ago by 65k • written 4.4 years ago by ▴ 730
0
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1
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1.4k
views
DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2 comparison design paired treatment
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by • 0
0
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4
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1.7k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
4.5 years ago luciest.rodriguez • 0
0
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2
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806
views
different designs for finding DEG by limma
limma DEG design
4.6 years ago amin.ghareyazi • 0
50 results • Page 1 of 1
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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