Showing : interactions • reset
1
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617
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Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 15 months ago by 41k • written 15 months ago by • 0
0
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2
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996
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DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 2.5 years ago by ★ 1.3k • written 2.5 years ago by • 0
0
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1
reply
609
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
0
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2
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770
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results() function and finding the difference of differences
interactions DESeq2
2.5 years ago Nayrouz • 0
0
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3
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877
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Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
1
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2
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1.4k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
3.2 years ago Dan ▴ 20
2
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3
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994
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DeSEQ2 factor effect without interaction effect
DESeq2 Interactions
3.3 years ago • updated 3.2 years ago cossardg ▴ 10
2
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3
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7.4k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by ▴ 30
6
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8
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2.4k
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Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 3.3 years ago by • 0 • written 6.5 years ago by ▴ 60
3
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3
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1.1k
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Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 3.6 years ago by 50k • written 3.6 years ago by ▴ 10
1
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5
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856
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Testing Interactions without an interaction term in the design formula
deseq2 interactions
updated 5.1 years ago by 41k • written 5.1 years ago by ▴ 30
0
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4
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1.9k
views
DESeq2 lfcShrink with interactions
deseq2 lfcShrink interactions
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
0
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5
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1.2k
views
Splitting a dataset and control sample batch
deseq2 interactions batch effect correction grouping variable
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 90
0
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5
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1.4k
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RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 10
0
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3
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1.1k
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DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 5.7 years ago by 41k • written 5.7 years ago by • 0
0
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2
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923
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Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq edgeR makecontrasts interactions
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 90
0
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1
reply
945
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.8 years ago by 65k • written 5.8 years ago by • 0
1
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5
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1.3k
views
Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
6.0 years ago David R ▴ 90
0
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1
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1.3k
views
Using Effect Coding or Orthogonal Coding instead of dummy coding in DESeq2?
deseq2 multiple factor design interactions orthogonal coding effect coding
updated 6.4 years ago by ★ 3.0k • written 6.4 years ago by ▴ 20
0
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2
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1.5k
views
stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
updated 6.4 years ago by 41k • written 8.4 years ago by ★ 1.5k
8
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3
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3.0k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 50
5
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4
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1.4k
views
Differential expression analysis desgin
differential expression deseq2 edger interactions limma
updated 6.6 years ago by 50k • written 6.6 years ago by ▴ 10
0
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2
replies
1.6k
views
DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 6.7 years ago by 41k • written 6.7 years ago by ▴ 10
3
votes
7
replies
2.8k
views
DESeq2 lfcShrink with interactions
deseq2 interactions logfoldchange
updated 6.7 years ago by 41k • written 6.7 years ago by ▴ 70
4
votes
1
reply
2.4k
views
Limma: Contrasts with interaction term
limma interactions continuous term multiple factor design
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 10
8
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3
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2.7k
views
[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
7.6 years ago lanhuong ▴ 20
3
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5
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4.3k
views
DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 7.7 years ago by 41k • written 7.7 years ago by ▴ 10
2
votes
6
replies
1.8k
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 8.0 years ago by 41k • written 8.0 years ago by ▴ 10
2
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4
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5.4k
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Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.1 years ago dwzhang.wisc ▴ 20
3
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7
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4.3k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 8.1 years ago by 50k • written 8.1 years ago by ▴ 90
2
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5
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1.8k
views
How to make sense of the fold change values in the interaction results object.
deseq2 logfoldchange interactions
updated 8.1 years ago by 41k • written 8.1 years ago by ▴ 30
2
votes
5
replies
5.5k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.3 years ago • updated 8.2 years ago rclaire ▴ 20
13
votes
6
replies
7.1k
views
DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
updated 8.3 years ago by 41k • written 8.3 years ago by ▴ 290
1
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5
replies
3.3k
views
Contrast All Interaction Effects in DESeq2 in current version (1.10.1)
DESeq2 differential gene expression interactions
8.5 years ago marcus.stoiber • 0
0
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2
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1.2k
views
R package for molecule interactions?
r package function interactions
8.5 years ago amyfm ▴ 10
6
votes
3
replies
5.4k
views
Calculating contrasts for continuous variable anad interaction effect in Limma
limma design matrix design and contrast matrix continuous interactions
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 20
0
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1
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1.6k
views
DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2 design and contrast matrix interactions contrast
updated 8.6 years ago by 41k • written 8.6 years ago by ▴ 20
2
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8
replies
3.1k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
8.9 years ago shao ▴ 100
1
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1
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1.5k
views
Interaction of fixed effects in DESeq2
deseq2 interactions
updated 8.9 years ago by 41k • written 8.9 years ago by • 0
3
votes
4
replies
3.0k
views
RNAseq analysis using edgeR - specifying and testing full factorial 2x2x4 model, main effects and interactions.
edger multiple factor design interactions
updated 9.0 years ago by ★ 28k • written 9.0 years ago by • 0
1
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0
replies
2.0k
views
Job: Bioinformatics / Biostatistics in genetic interaction analysis
high-throughput screening interactions genetics jobs image analysis Job
9.0 years ago Bernd Fischer ▴ 550
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 9.2 years ago by 41k • written 9.2 years ago by ▴ 90
0
votes
3
replies
1.9k
views
DESeq2: interaction controlling for genetic effects
deseq interactions
updated 9.4 years ago by 41k • written 9.4 years ago by ▴ 10
1
vote
7
replies
2.7k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
9.5 years ago pshannon ▴ 100
44 results • Page 1 of 1
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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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