Showing : Design • reset
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edgeR - design a complex matrix
design model.matrix edgeR complexdesign
updated 15 months ago by 53k • written 15 months ago by • 0
3
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3
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1.2k
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 18 months ago by 53k • written 18 months ago by • 0
0
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6
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1.2k
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 19 months ago by ★ 1.4k • written 19 months ago by ▴ 130
2
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3
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1.1k
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 20 months ago by 53k • written 20 months ago by • 0
2
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2
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850
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
20 months ago Sabiha ▴ 20
2
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2
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776
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Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
22 months ago • updated 21 months ago SamGG ▴ 360
3
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6
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1.6k
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
3
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9
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3.5k
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Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
2.7 years ago mohammedtoufiq91 ▴ 10
6
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11
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2.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.8 years ago mohammedtoufiq91 ▴ 10
2
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2
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1.4k
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Updating DESeq2 object's design with sva output
DESeq2 design sva
2.8 years ago Hatchet • 0
3
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6
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1.9k
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
3.0 years ago mohammedtoufiq91 ▴ 10
1
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2
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1.3k
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
3.0 years ago mohammedtoufiq91 ▴ 10
1
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2
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1.3k
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
3.0 years ago mohammedtoufiq91 ▴ 10
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13
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3.6k
views
DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 3.0 years ago by 43k • written 3.1 years ago by ▴ 10
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5
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1.8k
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Inquiry about suitable package for proteomics study design
Proteomics design
updated 3.1 years ago by • 0 • written 3.1 years ago by • 0
2
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5
replies
4.6k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 3.1 years ago by 43k • written 4.4 years ago by • 0
0
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1
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987
views
Design Matrix Singularity Error
DES DESIGN
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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2
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1.1k
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Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
2
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2
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2.7k
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Handling NA values in limma's voom design matrix
limma voom design NAs
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 10
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4
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1.6k
views
DESeq2 pseudotime series design?
DESeq2 design
3.7 years ago jordi.planells • 0
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2
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1.3k
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DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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1
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1.2k
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
1
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1
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1.2k
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Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
1
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2
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1.6k
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
4.0 years ago Barista • 0
0
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2
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1.5k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 4.0 years ago by ★ 1.4k • written 4.1 years ago by • 0
0
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1
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963
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
0
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2
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1.6k
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Design formula in DESeq2
model BatchEffect hidden Design DESeq2
4.1 years ago m.glymenaki • 0
2
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3
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2.1k
views
Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
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1
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2.7k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
0
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1
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1.4k
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Subject paired DESeq2 design
DESeq2 paired design
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 10
0
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1
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1.1k
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[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 4.3 years ago by 43k • written 4.4 years ago by • 0
2
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3
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1.8k
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Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 4.5 years ago by 53k • written 4.5 years ago by • 0
2
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3
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11k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 4.9 years ago by ★ 4.0k • written 4.9 years ago by ▴ 30
0
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1
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1.1k
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 50
2
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3
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1.3k
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
0
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5
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2.6k
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DESeq2 issue with hierarchical clustering
deseq2 design
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by • 0
2
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5
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1.7k
views
Picking the right design formula
deseq2 design experiment
5.2 years ago donnenfieldjonah • 0
4
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5
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4.2k
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How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
2
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8
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6.0k
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Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
5.3 years ago Pietro ▴ 40
4
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7
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1.8k
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 5.4 years ago by 53k • written 5.4 years ago by • 0
0
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1
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1.3k
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 5.5 years ago by 53k • written 5.5 years ago by • 0
2
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7
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3.0k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 5.5 years ago by 53k • written 5.5 years ago by • 0
6
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6
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1.9k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 5.8 years ago by ★ 13k • written 5.8 years ago by • 0
0
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10
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4.1k
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DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 5.8 years ago by ★ 1.4k • written 5.8 years ago by • 0
1
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4
replies
1.3k
views
Help with Deseq2 design
deseq2 design multifactor
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
1
vote
1
reply
28k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ★ 1.5k
0
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2
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1.7k
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
2
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1
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1.9k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 5.9 years ago by ▴ 60 • written 5.9 years ago by ★ 1.5k
1
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10
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11k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 4 months ago by 43k • written 6.0 years ago by • 0
1
vote
6
replies
2.3k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 6.0 years ago by 68k • written 6.0 years ago by ▴ 760
93 results • Page 1 of 2
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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