Showing : Interactions • reset
13
votes
6
replies
7.5k
views
DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
updated 9.0 years ago by 43k • written 9.0 years ago by ▴ 290
11
votes
3
replies
3.7k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 60
8
votes
3
replies
3.1k
views
[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
8.3 years ago lanhuong ▴ 20
6
votes
8
replies
3.1k
views
Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 4.0 years ago by • 0 • written 7.2 years ago by ▴ 60
6
votes
3
replies
5.8k
views
Calculating contrasts for continuous variable anad interaction effect in Limma
limma design matrix design and contrast matrix continuous interactions
updated 9.2 years ago by ★ 28k • written 9.2 years ago by ▴ 20
5
votes
4
replies
1.7k
views
Differential expression analysis desgin
differential expression deseq2 edger interactions limma
updated 7.3 years ago by 52k • written 7.3 years ago by ▴ 10
5
votes
11
replies
11k
views
DESeq2: with multiple factors and interaction terms won't show all effects
deseq2 multiple factor design contrast interactions
updated 9.9 years ago by 43k • written 9.9 years ago by ▴ 110
4
votes
1
reply
2.6k
views
Limma: Contrasts with interaction term
limma interactions continuous term multiple factor design
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 10
3
votes
7
replies
4.7k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 8.8 years ago by 52k • written 8.8 years ago by ▴ 90
3
votes
3
replies
1.3k
views
Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 4.3 years ago by 52k • written 4.3 years ago by ▴ 10
3
votes
4
replies
3.2k
views
RNAseq analysis using edgeR - specifying and testing full factorial 2x2x4 model, main effects and interactions.
edger multiple factor design interactions
updated 9.7 years ago by ★ 28k • written 9.7 years ago by • 0
3
votes
5
replies
4.6k
views
DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 8.4 years ago by 43k • written 8.5 years ago by ▴ 10
3
votes
7
replies
3.0k
views
DESeq2 lfcShrink with interactions
deseq2 interactions logfoldchange
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 70
2
votes
4
replies
6.0k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.8 years ago dwzhang.wisc ▴ 20
2
votes
6
replies
2.1k
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 8.7 years ago by 43k • written 8.7 years ago by ▴ 10
2
votes
5
replies
2.0k
views
How to make sense of the fold change values in the interaction results object.
deseq2 logfoldchange interactions
updated 8.8 years ago by 43k • written 8.8 years ago by ▴ 30
2
votes
3
replies
1.2k
views
DeSEQ2 factor effect without interaction effect
DESeq2 Interactions
4.0 years ago cossardg ▴ 10
2
votes
8
replies
3.3k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
9.6 years ago shao ▴ 100
2
votes
5
replies
5.9k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
9.0 years ago rclaire ▴ 20
2
votes
3
replies
9.7k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by ▴ 30
1
vote
1
reply
804
views
Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
1
vote
0
replies
2.2k
views
Job: Bioinformatics / Biostatistics in genetic interaction analysis
high-throughput screening interactions genetics jobs image analysis Job
9.8 years ago Bernd Fischer ▴ 550
1
vote
1
reply
1.7k
views
Interaction of fixed effects in DESeq2
deseq2 interactions
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
1
vote
5
replies
3.8k
views
Contrast All Interaction Effects in DESeq2 in current version (1.10.1)
DESeq2 differential gene expression interactions
9.2 years ago marcus.stoiber • 0
1
vote
5
replies
1.5k
views
Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
6.8 years ago David R ▴ 90
1
vote
5
replies
1.1k
views
Testing Interactions without an interaction term in the design formula
deseq2 interactions
updated 5.8 years ago by 43k • written 5.8 years ago by ▴ 30
1
vote
2
replies
1.6k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
3.9 years ago Dan ▴ 20
1
vote
7
replies
3.0k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
10.2 years ago pshannon ▴ 100
0
votes
1
reply
1.1k
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 6.6 years ago by 67k • written 6.6 years ago by • 0
0
votes
2
replies
1.1k
views
Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq edgeR makecontrasts interactions
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 90
0
votes
3
replies
1.3k
views
DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
0
votes
5
replies
1.6k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
0
votes
5
replies
1.5k
views
Splitting a dataset and control sample batch
deseq2 interactions batch effect correction grouping variable
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 110
0
votes
4
replies
2.3k
views
DESeq2 lfcShrink with interactions
deseq2 lfcShrink interactions
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
1
reply
787
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
votes
2
replies
1.4k
views
R package for molecule interactions?
r package function interactions
9.2 years ago amyfm ▴ 10
0
votes
1
reply
1.8k
views
DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2 design and contrast matrix interactions contrast
updated 9.3 years ago by 43k • written 9.3 years ago by ▴ 20
0
votes
3
replies
2.1k
views
DESeq2: interaction controlling for genetic effects
deseq interactions
updated 10.1 years ago by 43k • written 10.1 years ago by ▴ 10
0
votes
3
replies
1.2k
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
votes
2
replies
1.3k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 3.2 years ago by ★ 1.4k • written 3.2 years ago by • 0
0
votes
2
replies
1.9k
views
DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 10
0
votes
2
replies
1.7k
views
stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
updated 7.2 years ago by 43k • written 9.2 years ago by ★ 1.5k
0
votes
1
reply
1.5k
views
Using Effect Coding or Orthogonal Coding instead of dummy coding in DESeq2?
deseq2 multiple factor design interactions orthogonal coding effect coding
updated 7.1 years ago by ★ 3.0k • written 7.1 years ago by ▴ 20
0
votes
2
replies
992
views
results() function and finding the difference of differences
interactions DESeq2
3.2 years ago Nayrouz • 0
44 results • Page 1 of 1
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Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D by Michael Love 43k
hi, for questions about what statistical analysis approach to use, I recommend you work with a local statistician or someone familiar with …
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
I'm not certain that this will work with Oarfish, the documentation only mentions Salmon and piscem. I'd use tximport for now.
Answer: Problems with oarfish + tximport + swish by Michael Love 43k
> This is fine Did tximeta() print that a matching transcriptome was found?
Answer: DESeq2 Heatmap by swbarnes2 ★ 1.4k
> However, I've been asked why the first column (vehicle/control) isn't > entirely zero on the log fold change (logFC) expression scale. …
Comment: Biomart and ensembl not working? by James W. MacDonald 67k
``` > library(biomaRt) > mart <- useEnsembl("ensembl","hsapiens_gene_ensembl") Ensembl site unresponsive, trying useast mirror > mart Objec…
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Answer: Limma Interaction Effect with Covariates
Comment: DESeq2 for single cell pseudobulk processing
C: Limma: how to get same output as topTable but for all the genes ?
A: Processing agilent data by limma
A: Linear regression in DESeq2
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