Showing : interactions • reset
1
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498
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Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 11 months ago by 41k • written 11 months ago by • 0
0
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2
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877
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DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 2.1 years ago by ★ 1.3k • written 2.1 years ago by • 0
0
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1
reply
516
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Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 2.1 years ago by 41k • written 2.1 years ago by • 0
0
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2
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676
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results() function and finding the difference of differences
interactions DESeq2
2.1 years ago Nayrouz • 0
0
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3
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762
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Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
1
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2
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1.2k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
2.8 years ago Dan ▴ 20
2
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3
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887
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DeSEQ2 factor effect without interaction effect
DESeq2 Interactions
2.9 years ago cossardg ▴ 10
2
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3
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6.2k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 2.9 years ago by 3.9k • written 2.9 years ago by ▴ 20
6
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8
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2.1k
views
Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 3.0 years ago by • 0 • written 6.1 years ago by ▴ 60
3
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3
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974
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Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 3.2 years ago by 49k • written 3.2 years ago by ▴ 10
1
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5
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748
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Testing Interactions without an interaction term in the design formula
deseq2 interactions
updated 4.7 years ago by 41k • written 4.7 years ago by ▴ 30
0
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4
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1.7k
views
DESeq2 lfcShrink with interactions
deseq2 lfcShrink interactions
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
0
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5
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1.1k
views
Splitting a dataset and control sample batch
deseq2 interactions batch effect correction grouping variable
updated 5.2 years ago by 41k • written 5.2 years ago by ▴ 90
0
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5
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1.2k
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RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 5.2 years ago by 41k • written 5.2 years ago by ▴ 10
0
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3
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1.0k
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DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
0
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2
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833
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Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq edgeR makecontrasts interactions
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 70
0
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1
reply
846
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.5 years ago by 64k • written 5.5 years ago by • 0
1
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5
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1.1k
views
Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
5.7 years ago David R ▴ 70
0
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1
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1.2k
views
Using Effect Coding or Orthogonal Coding instead of dummy coding in DESeq2?
deseq2 multiple factor design interactions orthogonal coding effect coding
updated 6.0 years ago by ★ 2.8k • written 6.0 years ago by ▴ 20
0
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2
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1.4k
views
stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
updated 6.1 years ago by 41k • written 8.1 years ago by ★ 1.5k
8
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3
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2.7k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 6.2 years ago by 41k • written 6.2 years ago by ▴ 50
5
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4
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1.3k
views
Differential expression analysis desgin
differential expression deseq2 edger interactions limma
updated 6.2 years ago by 49k • written 6.2 years ago by ▴ 10
0
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2
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1.5k
views
DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 6.3 years ago by 41k • written 6.3 years ago by ▴ 10
3
votes
7
replies
2.6k
views
DESeq2 lfcShrink with interactions
deseq2 interactions logfoldchange
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 70
4
votes
1
reply
2.3k
views
Limma: Contrasts with interaction term
limma interactions continuous term multiple factor design
updated 6.8 years ago by ★ 28k • written 6.8 years ago by ▴ 10
8
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3
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2.5k
views
[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
7.2 years ago lanhuong ▴ 20
3
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5
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4.2k
views
DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 7.3 years ago by 41k • written 7.4 years ago by ▴ 10
2
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6
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1.7k
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 7.6 years ago by 41k • written 7.6 years ago by ▴ 10
2
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4
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5.1k
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Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
7.7 years ago dwzhang.wisc ▴ 20
3
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7
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4.1k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 7.7 years ago by 49k • written 7.7 years ago by ▴ 70
2
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5
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1.6k
views
How to make sense of the fold change values in the interaction results object.
deseq2 logfoldchange interactions
updated 7.7 years ago by 41k • written 7.7 years ago by ▴ 30
2
votes
5
replies
5.3k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
7.9 years ago rclaire ▴ 20
13
votes
6
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6.8k
views
DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
updated 7.9 years ago by 41k • written 7.9 years ago by ▴ 290
1
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5
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3.0k
views
Contrast All Interaction Effects in DESeq2 in current version (1.10.1)
DESeq2 differential gene expression interactions
8.1 years ago marcus.stoiber • 0
0
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2
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1.1k
views
R package for molecule interactions?
r package function interactions
8.1 years ago amyfm ▴ 10
6
votes
3
replies
5.2k
views
Calculating contrasts for continuous variable anad interaction effect in Limma
limma design matrix design and contrast matrix continuous interactions
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
0
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1
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1.5k
views
DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2 design and contrast matrix interactions contrast
updated 8.2 years ago by 41k • written 8.2 years ago by ▴ 20
2
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8
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3.0k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
8.5 years ago shao ▴ 100
1
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1
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1.4k
views
Interaction of fixed effects in DESeq2
deseq2 interactions
updated 8.5 years ago by 41k • written 8.5 years ago by • 0
3
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4
replies
2.8k
views
RNAseq analysis using edgeR - specifying and testing full factorial 2x2x4 model, main effects and interactions.
edger multiple factor design interactions
updated 8.6 years ago by ★ 28k • written 8.6 years ago by • 0
1
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0
replies
1.9k
views
Job: Bioinformatics / Biostatistics in genetic interaction analysis
high-throughput screening interactions genetics jobs image analysis Job
8.7 years ago Bernd Fischer ▴ 550
5
votes
11
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10k
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DESeq2: with multiple factors and interaction terms won't show all effects
deseq2 multiple factor design contrast interactions
updated 8.8 years ago by 41k • written 8.8 years ago by ▴ 90
0
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3
replies
1.8k
views
DESeq2: interaction controlling for genetic effects
deseq interactions
updated 9.0 years ago by 41k • written 9.0 years ago by ▴ 10
1
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7
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2.6k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
9.1 years ago pshannon ▴ 100
44 results • Page 1 of 1
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Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance by samer • 0
This is the result i got when i only looked on day 04 for the gene in example 1 posted above dds_sub <- dds[, dds$date %in% c("day04"…
Answer: What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE) by James W. MacDonald 64k
There are two types of probes used by Illumina. The type I probes bind directly to the CpG site and have two different probes (one for a me…
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance by Michael Love 41k
Then for the remaining genes that you don't think are DE, just plot like this: ``` dds_sub <- dds[,dds$condition %in% c("x","y")] dropleve…
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance by samer • 0
yes i turned it off @mikelove
Answer: autonomics: example("read_somascan", package = "autonomics") fails, but not on B by Mike Smith ★ 6.2k
It looks like `autonomics` uses `BiocFileCache` to create a local copy of the data and save repeat downloading. Given the (relatively) rec…
Votes
Answer: What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)
Answer: WGCNA documentation not available
Comment: Can the limma package be applied to Log2 RUV-normalized data?
Comment: Can the limma package be applied to Log2 RUV-normalized data?
Answer: Correct the batch effect in methylation analysis in R
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