Showing : design • reset
7
votes
7
replies
8.7k
views
DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2 LRT rnaseq design reduced model
updated 5.4 years ago by • 0 • written 7.0 years ago by ▴ 50
6
votes
6
replies
2.8k
views
design matrix for 4 groups in edgeR
edger design
9.5 years ago alakatos ▴ 130
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
6
votes
6
replies
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
5
votes
6
replies
1.6k
views
How to set up appropriate analysis using sample type and condition for DESeq2
deseq2 differential gene expression design
updated 5.5 years ago by 41k • written 5.6 years ago by • 0
4
votes
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
4
votes
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
4
votes
3
replies
6.9k
views
deseq2 warning for the design formula
deseq2 design
updated 8.2 years ago by 41k • written 8.2 years ago by ★ 1.5k
4
votes
13
replies
2.5k
views
Which formula should I use to set the best model matrix for my analysis ?
DESEQ2 EDGER design
7.6 years ago ZheFrench ▴ 50
4
votes
7
replies
3.2k
views
LIMMA time series spline model.matrix design setup
limma design model.matrix time series splines
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
4
votes
18
replies
24k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 4.8 years ago by • 0 • written 9.5 years ago by ▴ 100
3
votes
3
replies
788
views
Extracting within subject effect in a between and within subject model with DESeq2
deseq2 design
updated 5.1 years ago by 41k • written 5.1 years ago by ▴ 40
3
votes
4
replies
1.3k
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger design matrix de
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 10
3
votes
6
replies
2.7k
views
Limma design/contrast correct?
limma microarray design paired mixed model
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
3
votes
6
replies
842
views
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
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
3
votes
13
replies
2.2k
views
Design and independent filtering of patient RNA-seq data
differential gene expression deseq2 design independent filtering limma
updated 8.9 years ago by 65k • written 8.9 years ago by ▴ 90
3
votes
9
replies
1.8k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
13 months ago mohammedtoufiq91 ▴ 10
3
votes
4
replies
2.1k
views
Deseq2 DE between WT and MUTANT normalised with respect to control
deseq2 multiple factor design design and contrast matrix design multifactorial design
7.6 years ago shimbalama • 0
3
votes
7
replies
1.8k
views
DESeq2 design formula: how to account for twin data (MZ and DZ)?
DESeq2 twins design formula RNA-seq
6.5 years ago Simone • 0
3
votes
5
replies
1.4k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 40
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
votes
8
replies
2.4k
views
DESeq design question
deseq2 design
9.5 years ago • updated 9.1 years ago sunkid • 0
2
votes
3
replies
2.9k
views
Help with DESeq2 Multiple Factor Design
deseq2 design multiple factor design
updated 9.1 years ago by ▴ 610 • written 9.1 years ago by • 0
2
votes
4
replies
1.2k
views
design microarrays limma
limma statistical power design variability microarray
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
2
votes
4
replies
923
views
Limma model for paired and pool together
limma design rnaseq
updated 6.0 years ago by ★ 7.9k • written 6.0 years ago by ▴ 360
2
votes
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
2
votes
7
replies
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
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
2
votes
5
replies
1.1k
views
Picking the right design formula
deseq2 design experiment
3.6 years ago donnenfieldjonah • 0
2
votes
3
replies
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
2
votes
3
replies
7.5k
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
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
votes
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
2
votes
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
2
votes
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
votes
2
replies
290
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
12 weeks ago SamGG ▴ 350
2
votes
3
replies
293
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
837
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
14 months ago Hatchet • 0
2
votes
3
replies
1.3k
views
how to set design for 2-dye Agilent array experiment with common reference group?
limma 2-dye agilent common reference design
updated 8.4 years ago by 65k • written 8.4 years ago by ★ 3.9k
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
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
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
798
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
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
1
vote
1
reply
942
views
Best formula to use for this experimental setup
deseq2 differential gene expression design
updated 8.9 years ago by 41k • written 8.9 years ago by • 0
1
vote
8
replies
1.5k
views
design versus interaction term similarities and/or differences?
deseq2 ANOVA design interaction term
updated 6.2 years ago by 41k • written 6.2 years ago by • 0
1
vote
2
replies
1.6k
views
DESeq2 - Design for TCGA unpaired RNAseq data
DESeq2 design TCGA unpaired RNAseq
updated 6.3 years ago by 41k • written 6.3 years ago by ▴ 10
1
vote
2
replies
952
views
DESeq2 design with different cell lines and disease status
deseq2 design
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
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
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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