Showing : DESIGN • reset
1
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25k
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lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 4.3 years ago by 42k • written 4.3 years ago by ★ 1.5k
4
votes
18
replies
24k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 4.9 years ago by • 0 • written 9.5 years ago by ▴ 100
7
votes
7
replies
8.7k
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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
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 3.4 years ago by ▴ 30
1
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8
replies
7.2k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 3.4 years ago by 42k • written 4.5 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 42k • written 8.2 years ago by ★ 1.5k
1
vote
1
reply
5.7k
views
Not full rank design using Deseq2
deseq2 design counts
updated 9.2 years ago by 42k • written 9.2 years ago by ▴ 30
2
votes
8
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4.3k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
3.7 years ago Pietro ▴ 40
0
votes
3
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3.4k
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Where to include an interaction term in DESeq2
deseq2 contrast design
updated 9.3 years ago by 42k • written 9.3 years ago by • 0
2
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5
replies
3.3k
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DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 18 months ago by 42k • written 2.9 years ago by • 0
4
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7
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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
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
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
6
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6
replies
2.8k
views
design matrix for 4 groups in edgeR
edger design
9.5 years ago alakatos ▴ 130
3
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6
replies
2.7k
views
Limma design/contrast correct?
limma microarray design paired mixed model
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
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
0
votes
10
replies
2.4k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 4.3 years ago by ★ 1.4k • written 4.3 years ago by • 0
2
votes
8
replies
2.4k
views
DESeq design question
deseq2 design
9.5 years ago • updated 9.2 years ago sunkid • 0
3
votes
13
replies
2.3k
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
0
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13
replies
2.1k
views
DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 18 months ago by 42k • written 19 months ago by ▴ 10
3
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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
2
votes
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
0
votes
8
replies
2.0k
views
Two controls in RNAseq formula for DESeq2
deseq2 formula controls design
updated 4.7 years ago by 42k • written 4.7 years ago by • 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
6.6 years ago • updated 6.5 years ago Simone • 0
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
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 42k • written 2.7 years ago by • 0
0
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4
replies
1.7k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
4.6 years ago luciest.rodriguez • 0
0
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5
replies
1.7k
views
DESeq2 issue with hierarchical clustering
deseq2 design
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
0
votes
2
replies
1.7k
views
DESeq2- multifactor design- 3 conditions and 3 timepoints
deseq2 design
updated 5.3 years ago by 42k • written 5.3 years ago by • 0
1
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2
replies
1.7k
views
DESeq2 - Design for TCGA unpaired RNAseq data
DESeq2 design TCGA unpaired RNAseq
updated 6.3 years ago by 42k • written 6.3 years ago by ▴ 10
0
votes
5
replies
1.6k
views
Limma: how to account for twin data (both MZ and DZ twins)?
limma design RNA-seq formula twins
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
0
votes
1
reply
1.6k
views
intra-sample time series comparison using DESeq2
deseq2 time course rnaseq design contrast
updated 7.2 years ago by 42k • written 7.2 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 5.6 years ago by 42k • written 5.6 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
0
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7
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1.5k
views
Problems with DESeq2 'design' parameter using Shiny/rhandsontable
deseq2 shiny design rhandsontable hot_to_r()
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
0
votes
0
replies
1.5k
views
Job: Come apply for our Epidemiologist, AncestryHealth role
genomics genetics design statistics scientist Job
8.9 years ago careers • 0
1
vote
8
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1.5k
views
design versus interaction term similarities and/or differences?
deseq2 ANOVA design interaction term
updated 6.2 years ago by 42k • written 6.2 years ago by • 0
1
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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
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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 ★ 1.4k • written 4.5 years ago by • 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
0
votes
5
replies
1.4k
views
DESeq2 It is correct to use interaction term for patient variability?
deseq2 design interaction term R
6.2 years ago briverog • 0
6
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11
replies
1.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
15 months ago mohammedtoufiq91 ▴ 10
2
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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
0
votes
7
replies
1.3k
views
DeSeq2 Ribosome Profiling: multiple factor design
deseq2 design timeseries
updated 5.3 years ago by 42k • written 5.3 years ago by ▴ 20
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
2
votes
3
replies
1.3k
views
Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
0
votes
5
replies
1.3k
views
DESeq2 design formula - correlation with ordered variable
DESeq2 design formula matrix
updated 5.9 years ago by 42k • written 5.9 years ago by ▴ 170
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
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 3.0 years ago by • 0
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
50 results • Page 1 of 1
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Replies
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Comment: How to use spike-in information (sequences from another species) with DESeq2::DE by maria.soler • 0
Hi, I have a question barely related to this topic. Do you use a custom reference genome combining your organism and the one used as a spik…
Answer: Differential gene expression analysis results by ATpoint ★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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