Showing : interactions • reset
5
votes
11
replies
12k
views
DESeq2: with multiple factors and interaction terms won't show all effects
deseq2 multiple factor design contrast interactions
updated 10.9 years ago by 43k • written 10.9 years ago by ▴ 110
2
votes
3
replies
12k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 5.0 years ago by ★ 4.0k • written 5.1 years ago by ▴ 30
13
votes
6
replies
8.0k
views
DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
updated 10.0 years ago by 43k • written 10.0 years ago by ▴ 290
2
votes
4
replies
6.7k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
9.8 years ago dwzhang.wisc ▴ 20
6
votes
3
replies
6.3k
views
Calculating contrasts for continuous variable anad interaction effect in Limma
limma design matrix design and contrast matrix continuous interactions
updated 10.3 years ago by ★ 29k • written 10.3 years ago by ▴ 20
2
votes
5
replies
6.3k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
10.0 years ago rclaire ▴ 20
3
votes
7
replies
5.2k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 9.8 years ago by 53k • written 9.8 years ago by ▴ 90
3
votes
5
replies
5.1k
views
DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 9.4 years ago by 43k • written 9.5 years ago by ▴ 10
11
votes
3
replies
4.4k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 60
1
vote
5
replies
4.3k
views
Contrast All Interaction Effects in DESeq2 in current version (1.10.1)
DESeq2 differential gene expression interactions
10.2 years ago marcus.stoiber • 0
6
votes
8
replies
3.7k
views
Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 5.1 years ago by • 0 • written 8.2 years ago by ▴ 60
3
votes
4
replies
3.6k
views
RNAseq analysis using edgeR - specifying and testing full factorial 2x2x4 model, main effects and interactions.
edger multiple factor design interactions
updated 10.7 years ago by ★ 29k • written 10.7 years ago by • 0
2
votes
8
replies
3.6k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
10.6 years ago shao ▴ 100
3
votes
7
replies
3.5k
views
DESeq2 lfcShrink with interactions
deseq2 interactions logfoldchange
updated 8.5 years ago by 43k • written 8.5 years ago by ▴ 70
1
vote
7
replies
3.5k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
11.2 years ago pshannon ▴ 100
8
votes
3
replies
3.4k
views
[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
9.3 years ago lanhuong ▴ 20
4
votes
1
reply
2.9k
views
Limma: Contrasts with interaction term
limma interactions continuous term multiple factor design
updated 8.9 years ago by ★ 29k • written 8.9 years ago by ▴ 10
0
votes
4
replies
2.8k
views
DESeq2 lfcShrink with interactions
deseq2 lfcShrink interactions
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
2
votes
6
replies
2.5k
views
Seeking confirmation on manually setting contrasts for a 3-factor design in DESeq2 with multiple interaction terms
deseq2 multiple factor design interactions design and contrast matrix contrast
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 10
2
votes
5
replies
2.5k
views
How to make sense of the fold change values in the interaction results object.
deseq2 logfoldchange interactions
updated 9.8 years ago by 43k • written 9.8 years ago by ▴ 30
1
vote
0
replies
2.4k
views
Job: Bioinformatics / Biostatistics in genetic interaction analysis
high-throughput screening interactions genetics jobs image analysis Job
10.8 years ago Bernd Fischer ▴ 550
0
votes
3
replies
2.3k
views
DESeq2: interaction controlling for genetic effects
deseq interactions
updated 11.1 years ago by 43k • written 11.1 years ago by ▴ 10
0
votes
2
replies
2.3k
views
DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 8.4 years ago by 43k • written 8.4 years ago by ▴ 10
0
votes
1
reply
2.1k
views
DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2 design and contrast matrix interactions contrast
updated 10.3 years ago by 43k • written 10.3 years ago by ▴ 20
0
votes
2
replies
2.1k
views
stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
updated 8.2 years ago by 43k • written 10.2 years ago by ★ 1.5k
1
vote
2
replies
2.0k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
4.9 years ago Dan ▴ 20
5
votes
4
replies
1.9k
views
Differential expression analysis desgin
differential expression deseq2 edger interactions limma
updated 8.3 years ago by 53k • written 8.3 years ago by ▴ 10
0
votes
5
replies
1.9k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
1
vote
5
replies
1.9k
views
Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
7.8 years ago David R ▴ 90
1
vote
1
reply
1.9k
views
Interaction of fixed effects in DESeq2
deseq2 interactions
updated 10.6 years ago by 43k • written 10.6 years ago by • 0
0
votes
1
reply
1.8k
views
Using Effect Coding or Orthogonal Coding instead of dummy coding in DESeq2?
deseq2 multiple factor design interactions orthogonal coding effect coding
updated 8.1 years ago by ★ 3.0k • written 8.1 years ago by ▴ 20
0
votes
5
replies
1.8k
views
Splitting a dataset and control sample batch
deseq2 interactions batch effect correction grouping variable
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 110
0
votes
2
replies
1.6k
views
R package for molecule interactions?
r package function interactions
10.2 years ago amyfm ▴ 10
3
votes
3
replies
1.6k
views
Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 5.3 years ago by 53k • written 5.3 years ago by ▴ 10
0
votes
2
replies
1.6k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 4.2 years ago by ★ 1.4k • written 4.2 years ago by • 0
2
votes
3
replies
1.6k
views
DeSEQ2 factor effect without interaction effect
DESeq2 Interactions
5.0 years ago cossardg ▴ 10
0
votes
3
replies
1.6k
views
DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
votes
3
replies
1.6k
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
votes
2
replies
1.5k
views
Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq edgeR makecontrasts interactions
updated 7.6 years ago by ★ 29k • written 7.6 years ago by ▴ 90
1
vote
5
replies
1.3k
views
Testing Interactions without an interaction term in the design formula
deseq2 interactions
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 30
0
votes
1
reply
1.3k
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 7.6 years ago by 68k • written 7.6 years ago by • 0
0
votes
2
replies
1.3k
views
results() function and finding the difference of differences
interactions DESeq2
4.2 years ago Nayrouz • 0
1
vote
1
reply
1.1k
views
Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
1
reply
985
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
44 results • Page 1 of 1
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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