Showing : Interactions • reset
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Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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2
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1.3k
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DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by • 0
0
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1
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802
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Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
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2
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1.0k
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results() function and finding the difference of differences
interactions DESeq2
3.3 years ago Nayrouz • 0
0
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3
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1.3k
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Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
1
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2
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1.7k
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How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
4.0 years ago Dan ▴ 20
2
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3
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1.3k
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DeSEQ2 factor effect without interaction effect
DESeq2 Interactions
4.1 years ago cossardg ▴ 10
2
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3
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10k
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DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by ▴ 30
6
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8
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3.1k
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Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 4.1 years ago by • 0 • written 7.3 years ago by ▴ 60
3
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3
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1.3k
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Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 4.4 years ago by 52k • written 4.4 years ago by ▴ 10
1
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5
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1.1k
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Testing Interactions without an interaction term in the design formula
deseq2 interactions
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 30
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4
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2.3k
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DESeq2 lfcShrink with interactions
deseq2 lfcShrink interactions
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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5
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1.5k
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Splitting a dataset and control sample batch
deseq2 interactions batch effect correction grouping variable
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 110
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5
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1.7k
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RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 6.4 years ago by 43k • written 6.4 years ago by ▴ 10
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3
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1.3k
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DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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2
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1.2k
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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
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1
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1.1k
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Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
1
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5
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1.6k
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Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
6.9 years ago David R ▴ 90
0
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1
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1.5k
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Using Effect Coding or Orthogonal Coding instead of dummy coding in DESeq2?
deseq2 multiple factor design interactions orthogonal coding effect coding
updated 7.2 years ago by ★ 3.0k • written 7.2 years ago by ▴ 20
0
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2
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1.8k
views
stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
updated 7.3 years ago by 43k • written 9.3 years ago by ★ 1.5k
11
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3
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3.8k
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Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 60
5
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4
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1.7k
views
Differential expression analysis desgin
differential expression deseq2 edger interactions limma
updated 7.4 years ago by 52k • written 7.4 years ago by ▴ 10
0
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2
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1.9k
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DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 10
3
votes
7
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3.1k
views
DESeq2 lfcShrink with interactions
deseq2 interactions logfoldchange
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 70
4
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1
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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
8
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3
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3.1k
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[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
8.4 years ago lanhuong ▴ 20
3
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5
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4.6k
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DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 8.5 years ago by 43k • written 8.5 years ago by ▴ 10
2
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6
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2.1k
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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 8.8 years ago by 43k • written 8.8 years ago by ▴ 10
2
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4
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6.1k
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Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.9 years ago dwzhang.wisc ▴ 20
3
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7
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4.8k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 8.9 years ago by 52k • written 8.9 years ago by ▴ 90
2
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5
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2.0k
views
How to make sense of the fold change values in the interaction results object.
deseq2 logfoldchange interactions
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 30
2
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5
replies
5.9k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
9.1 years ago • updated 9.0 years ago rclaire ▴ 20
13
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6
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7.6k
views
DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
updated 9.1 years ago by 43k • written 9.1 years ago by ▴ 290
1
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5
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3.9k
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Contrast All Interaction Effects in DESeq2 in current version (1.10.1)
DESeq2 differential gene expression interactions
9.3 years ago marcus.stoiber • 0
0
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2
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1.4k
views
R package for molecule interactions?
r package function interactions
9.3 years ago amyfm ▴ 10
6
votes
3
replies
5.9k
views
Calculating contrasts for continuous variable anad interaction effect in Limma
limma design matrix design and contrast matrix continuous interactions
updated 9.3 years ago by ★ 28k • written 9.3 years ago by ▴ 20
0
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1
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1.9k
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DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2 design and contrast matrix interactions contrast
updated 9.4 years ago by 43k • written 9.4 years ago by ▴ 20
2
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8
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3.3k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
9.7 years ago shao ▴ 100
1
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1
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1.7k
views
Interaction of fixed effects in DESeq2
deseq2 interactions
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
3
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4
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3.2k
views
RNAseq analysis using edgeR - specifying and testing full factorial 2x2x4 model, main effects and interactions.
edger multiple factor design interactions
updated 9.8 years ago by ★ 28k • written 9.8 years ago by • 0
1
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0
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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
5
votes
11
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11k
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DESeq2: with multiple factors and interaction terms won't show all effects
deseq2 multiple factor design contrast interactions
updated 10.0 years ago by 43k • written 10.0 years ago by ▴ 110
0
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3
replies
2.1k
views
DESeq2: interaction controlling for genetic effects
deseq interactions
updated 10.2 years ago by 43k • written 10.2 years ago by ▴ 10
1
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7
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3.0k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
10.3 years ago pshannon ▴ 100
44 results • Page 1 of 1
Recent ...
Replies
Answer: SingleR with multiple single cell references by Aaron Lun ★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies by ATpoint ★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Answer: To count or not to count multi-overlapping reads? by Gordon Smyth 52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2? by ATpoint ★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2? by Wolfgang Huber ★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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Teacher to James W. MacDonald 68k
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