Showing : design • reset
0
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6
replies
188
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 1 day ago by ★ 1.3k • written 3 days ago by ▴ 130
2
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3
replies
294
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
2
votes
2
replies
262
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
2
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2
replies
291
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
12 weeks ago SamGG ▴ 350
3
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6
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843
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
3
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9
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1.8k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
13 months ago mohammedtoufiq91 ▴ 10
6
votes
11
replies
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
replies
838
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
14 months ago Hatchet • 0
3
votes
6
replies
996
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
16 months ago mohammedtoufiq91 ▴ 10
1
vote
2
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761
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Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
17 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
787
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
17 months ago mohammedtoufiq91 ▴ 10
0
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13
replies
2.1k
views
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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5
replies
1.0k
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 18 months ago by • 0 • written 18 months ago by • 0
2
votes
5
replies
3.2k
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DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 18 months ago by 41k • written 2.9 years ago by • 0
0
votes
1
reply
568
views
Design Matrix Singularity Error
DES DESIGN
updated 19 months ago by 41k • written 19 months ago by • 0
0
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2
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685
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Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 23 months ago by 41k • written 23 months ago by • 0
2
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2
replies
1.5k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 24 months ago by 50k • written 24 months ago by ▴ 10
0
votes
4
replies
990
views
DESeq2 pseudotime series design?
DESeq2 design
2.2 years ago jordi.planells • 0
0
votes
2
replies
861
views
DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 2.4 years ago by 41k • written 2.4 years ago by • 0
0
votes
1
reply
747
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
799
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
vote
2
replies
975
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
2.5 years ago Barista • 0
0
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2
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1.0k
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
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1
reply
615
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
replies
941
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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
replies
1.3k
views
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
votes
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
votes
1
reply
953
views
Subject paired DESeq2 design
DESeq2 paired design
updated 2.8 years ago by 41k • written 2.8 years ago by ▴ 10
0
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1
reply
695
views
[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 2.8 years ago by 41k • written 2.8 years ago by • 0
2
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3
replies
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
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3
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7.5k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 3.3 years ago by ★ 3.9k • written 3.4 years ago by ▴ 30
0
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1
reply
754
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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836
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
replies
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
803
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
views
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
vote
4
replies
822
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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972
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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
reply
1.3k
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
vote
8
replies
7.2k
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
replies
1.5k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 4.5 years ago by 65k • written 4.5 years ago by ▴ 730
0
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1
reply
1.5k
views
DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2 comparison design paired treatment
updated 4.5 years ago by ★ 1.3k • written 4.5 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
4.6 years ago luciest.rodriguez • 0
50 results • Page 1 of 1
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Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 with no issues at all. If you're having trouble with Bioc installa…
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Thanks Gordon for the advice! I ran fgsea, gsva and camera(), the most significant pathways are different. For the purpose of finding pathw…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function? by Henrik Bengtsson ★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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