Showing : Interactions • reset
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30
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DeSEQ2 factor effect without interaction effect
DESeq2 Interactions
2 days ago cossardg • 0
2
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3
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105
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DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
19 days ago vanbelj • 10 • updated 12 days ago Kevin Blighe 2.3k
5
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8
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624
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Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
3.2 years ago rbronste • 60 • updated 19 days ago pierre.marin • 0
3
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3
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176
Views
Problem to understand Interactions at any time
RNA-seq edgeR interactions
3 months ago vm.higareda • 10 • updated 3 months ago Gordon Smyth 41k
1
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5
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210
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Testing Interactions without an interaction term in the design formula
deseq2 interactions
21 months ago colaneri • 30 • updated 21 months ago Michael Love 31k
0
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4
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402
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DESeq2 lfcShrink with interactions
deseq2 lfcShrink interactions
23 months ago hannepainter • 0 • updated 23 months ago Michael Love 31k
0
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5
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322
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Splitting a dataset and control sample batch
deseq2 interactions batch effect correction grouping variable
2.3 years ago mat.lesche • 80 • updated 2.3 years ago Michael Love 31k
0
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5
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387
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RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
2.3 years ago Maithê Barros • 10 • updated 2.3 years ago Michael Love 31k
0
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3
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333
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DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
2.4 years ago fargo • 0 • updated 2.4 years ago Michael Love 31k
0
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2
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315
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Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq edgeR makecontrasts interactions
2.6 years ago David Rengel • 70 • updated 2.6 years ago Aaron Lun ♦ 26k
0
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1
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316
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Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
2.6 years ago khill33 • 0 • updated 2.6 years ago James W. MacDonald 55k
1
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5
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419
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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
2.8 years ago David Rengel • 70
0
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1
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547
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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
3.1 years ago vlaufer • 0 • updated 3.1 years ago Peter Langfelder ♦ 2.6k
0
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2
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818
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stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
5.2 years ago Assa Yeroslaviz ♦ 1.5k • updated 3.2 years ago Michael Love 31k
5
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3
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929
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Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
3.3 years ago red_bricks • 20 • updated 3.3 years ago Michael Love 31k
5
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4
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540
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Differential expression analysis desgin
differential expression deseq2 edger interactions limma
3.3 years ago kendralec • 10 • updated 3.3 years ago Gordon Smyth 41k
0
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2
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866
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DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
3.4 years ago grashow • 0 • updated 3.4 years ago Michael Love 31k
3
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7
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1.3k
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DESeq2 lfcShrink with interactions
deseq2 interactions logfoldchange
3.5 years ago rrcutler • 50 • updated 3.5 years ago Michael Love 31k
4
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1
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1.6k
Views
Limma: Contrasts with interaction term
limma interactions continuous term multiple factor design
3.9 years ago huma • 10 • updated 3.9 years ago Aaron Lun ♦ 26k
6
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3
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1.2k
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[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
4.3 years ago lanhuong • 20
2
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5
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2.0k
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DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
4.5 years ago c.evang • 0 • updated 4.4 years ago Michael Love 31k
2
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6
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896
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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
4.7 years ago piensaglobalmente • 10 • updated 4.7 years ago Michael Love 31k
2
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4
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2.7k
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Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
4.8 years ago dwzhang.wisc • 20
3
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7
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2.4k
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edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
4.8 years ago David Rengel • 70 • updated 4.8 years ago Gordon Smyth 41k
2
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5
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1.1k
Views
How to make sense of the fold change values in the interaction results object.
deseq2 logfoldchange interactions
4.8 years ago colaneri • 30 • updated 4.8 years ago Michael Love 31k
0
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5
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3.1k
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DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
5.0 years ago rclaire • 0
9
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6
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4.5k
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DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
5.0 years ago Stephen Turner • 270 • updated 5.0 years ago Michael Love 31k
1
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5
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1.7k
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Contrast All Interaction Effects in DESeq2 in current version (1.10.1)
DESeq2 differential gene expression interactions
5.2 years ago marcus.stoiber • 0
0
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2
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599
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R package for molecule interactions?
r package function interactions
5.2 years ago amyfm • 10
5
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3
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3.7k
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Calculating contrasts for continuous variable anad interaction effect in Limma
limma design matrix design and contrast matrix continuous interactions
5.3 years ago jaison75 • 20 • updated 5.3 years ago Aaron Lun ♦ 26k
0
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1
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1.1k
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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
5.3 years ago moldach • 20 • updated 5.3 years ago Michael Love 31k
2
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8
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2.2k
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confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
5.6 years ago shao • 90
0
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1
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840
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Interaction of fixed effects in DESeq2
deseq2 interactions
5.6 years ago Silva • 0 • updated 5.6 years ago Michael Love 31k
3
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4
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1.9k
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RNAseq analysis using edgeR - specifying and testing full factorial 2x2x4 model, main effects and interactions.
edger multiple factor design interactions
5.7 years ago v.oostra • 0 • updated 5.7 years ago Aaron Lun ♦ 26k
1
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0
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1.3k
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Job: Bioinformatics / Biostatistics in genetic interaction analysis
high-throughput screening interactions genetics jobs image analysis Job
5.8 years ago Bernd Fischer • 540
5
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11
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8.1k
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DESeq2: with multiple factors and interaction terms won't show all effects
deseq2 multiple factor design contrast interactions
5.9 years ago mat.lesche • 80 • updated 5.9 years ago Michael Love 31k
0
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3
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1.4k
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DESeq2: interaction controlling for genetic effects
deseq interactions
6.1 years ago rachelwright8 • 10 • updated 6.1 years ago Michael Love 31k
1
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7
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1.7k
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Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
6.2 years ago pshannon • 90
38 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 Error: ncol(countData) == nrow(colData) is not TRUE by Pedram • 0
Hello Michael I could not make the same matrix although I did what you said
Comment: Replace a specific nucleotide sequence, at a specific position, with another in by Konstantinos Yeles • 40
Hello @Benjamin-24571 for your example, I can suggest you this code: Read <- c("1","2","3","4") Sequences <- c("ACACCCACG", "AA…
Comment: CHIP Seq Analysis by DiffBind Package by shrinka.genetics • 0
Hello Thanks for your reply. I changed my file format and now it ran. It gave one plot also. All file s are in same directory. No…
Answer: Installing Bioconductor packages in Docker by Konstantinos Yeles • 40
Hello, @adklts-21974 My way to do the installation of packages in a docker is like this: FROM bioconductor/bioconductor_docker…
Comment: HTqPCR: dealing with technical replicates (filterCategory) and inability to anal by larissa.stanberry • 0
I ran into the same issue. It appears that filtering does not carry over featureData with the exception of featureNames, e.g. call featureD…
Votes
A: single-cells RNA-seq analysis by MAST with unbalanced group size
single-cells RNA-seq analysis by MAST with unbalanced group size
A: single-cells RNA-seq analysis by MAST with unbalanced group size
A: DESeq2 1.20.0 lfcshrink function
DEXSeq Usage and Expression Confusion
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