Showing : design • reset
6
votes
6
replies
2.8k
views
design matrix for 4 groups in edgeR
edger design
9.5 years ago alakatos ▴ 130
2
votes
8
replies
2.4k
views
DESeq design question
deseq2 design
9.4 years ago • updated 9.1 years ago sunkid • 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
4
votes
13
replies
2.5k
views
Which formula should I use to set the best model matrix for my analysis ?
DESEQ2 EDGER design
7.5 years ago ZheFrench ▴ 40
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
6
votes
11
replies
1.3k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
14 months ago mohammedtoufiq91 ▴ 10
0
votes
3
replies
815
views
Analysis strategy - possible to use naive control group as t=0 for two treatment groups?
Deseq2 design time course basal group
updated 4.8 years ago by 41k • written 4.8 years ago by • 0
0
votes
8
replies
1.9k
views
Two controls in RNAseq formula for DESeq2
deseq2 formula controls design
updated 4.7 years ago by 41k • written 4.7 years ago by • 0
0
votes
2
replies
994
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
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
0
votes
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
votes
4
replies
1.7k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
4.5 years ago luciest.rodriguez • 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
2.8k
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
0
votes
5
replies
981
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 18 months ago by • 0 • written 18 months 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
0
votes
5
replies
1.4k
views
DESeq2 It is correct to use interaction term for patient variability?
deseq2 design interaction term R
6.1 years ago briverog • 0
2
votes
4
replies
914
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
0
votes
5
replies
1.3k
views
DESeq2 design formula - correlation with ordered variable
DESeq2 design formula matrix
updated 5.9 years ago by 41k • written 5.9 years ago by ▴ 170
5
votes
6
replies
1.5k
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 5.5 years ago by • 0
0
votes
7
replies
1.3k
views
DeSeq2 Ribosome Profiling: multiple factor design
deseq2 design timeseries
updated 5.3 years ago by 41k • written 5.3 years ago by ▴ 20
3
votes
6
replies
2.6k
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
0
votes
2
replies
1.6k
views
DESeq2- multifactor design- 3 conditions and 3 timepoints
deseq2 design
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
0
votes
1
reply
585
views
DESeq2 3 factor design - whether to split up data or add interaction terms
deseq2 design
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
0
votes
7
replies
1.5k
views
Problems with DESeq2 'design' parameter using Shiny/rhandsontable
deseq2 shiny design rhandsontable hot_to_r()
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
3
votes
4
replies
1.3k
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger design matrix de
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
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
3
votes
3
replies
778
views
Extracting within subject effect in a between and within subject model with DESeq2
deseq2 design
updated 5.0 years ago by 41k • written 5.0 years ago by ▴ 40
0
votes
1
reply
616
views
Perform time course rna seq analysis at once with a single design or separate differential analysis for each time point
deseq2 design
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
1
vote
1
reply
990
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2 differential expression batch correction design
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 40
0
votes
1
reply
634
views
DESeq2 analysis of multifactorial RNAseq experiment
deseq2 design time-course
updated 4.8 years ago by 41k • written 4.8 years ago by • 0
0
votes
1
reply
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
1
vote
6
replies
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
1
vote
8
replies
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
2
votes
1
reply
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
0
votes
2
replies
949
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
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
806
views
Help with Deseq2 design
deseq2 design multifactor
updated 4.2 years ago by 41k • written 4.2 years ago by • 0
0
votes
10
replies
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
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
2
votes
7
replies
1.9k
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
1
reply
790
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
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
0
votes
5
replies
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
votes
3
replies
824
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
votes
1
reply
745
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
0
votes
2
replies
921
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
2.5 years ago m.glymenaki • 0
2
votes
3
replies
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
votes
2
replies
669
views
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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