Showing : interactions • reset
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 42k • written 8.3 years ago by ▴ 290
8
votes
3
replies
2.7k
views
[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
7.6 years ago lanhuong ▴ 20
8
votes
3
replies
3.0k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 6.6 years ago by 42k • written 6.6 years ago by ▴ 50
6
votes
8
replies
2.5k
views
Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 3.4 years ago by • 0 • written 6.5 years ago by ▴ 60
6
votes
3
replies
5.5k
views
Calculating contrasts for continuous variable anad interaction effect in Limma
limma design matrix design and contrast matrix continuous interactions
updated 8.6 years ago by ★ 28k • written 8.6 years ago by ▴ 20
5
votes
4
replies
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
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 42k • written 9.2 years ago by ▴ 90
4
votes
1
reply
2.4k
views
Limma: Contrasts with interaction term
limma interactions continuous term multiple factor design
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 10
3
votes
7
replies
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
3
votes
3
replies
1.1k
views
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
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
3
votes
5
replies
4.3k
views
DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 7.7 years ago by 42k • written 7.8 years ago by ▴ 10
3
votes
7
replies
2.8k
views
DESeq2 lfcShrink with interactions
deseq2 interactions logfoldchange
updated 6.8 years ago by 42k • written 6.8 years ago by ▴ 70
2
votes
4
replies
5.4k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.1 years ago dwzhang.wisc ▴ 20
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 42k • written 8.0 years ago by ▴ 10
2
votes
5
replies
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 42k • written 8.1 years ago by ▴ 30
2
votes
3
replies
1.0k
views
DeSEQ2 factor effect without interaction effect
DESeq2 Interactions
3.3 years ago cossardg ▴ 10
2
votes
8
replies
3.1k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
8.9 years ago shao ▴ 100
2
votes
5
replies
5.5k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.3 years ago rclaire ▴ 20
2
votes
3
replies
7.5k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 3.3 years ago by ★ 3.9k • written 3.4 years ago by ▴ 30
1
vote
1
reply
628
views
Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 15 months ago by 42k • written 15 months ago by • 0
1
vote
0
replies
2.0k
views
Job: Bioinformatics / Biostatistics in genetic interaction analysis
high-throughput screening interactions genetics jobs image analysis Job
9.1 years ago Bernd Fischer ▴ 550
1
vote
1
reply
1.5k
views
Interaction of fixed effects in DESeq2
deseq2 interactions
updated 8.9 years ago by 42k • written 8.9 years ago by • 0
1
vote
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
1
vote
5
replies
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
6.1 years ago David R ▴ 90
1
vote
5
replies
866
views
Testing Interactions without an interaction term in the design formula
deseq2 interactions
updated 5.1 years ago by 42k • written 5.1 years ago by ▴ 30
1
vote
2
replies
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
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
0
votes
1
reply
952
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
0
votes
2
replies
932
views
Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq edgeR makecontrasts interactions
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 90
0
votes
3
replies
1.1k
views
DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 5.7 years ago by 42k • written 5.7 years ago by • 0
0
votes
5
replies
1.4k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 5.6 years ago by 42k • written 5.6 years ago by ▴ 10
0
votes
5
replies
1.3k
views
Splitting a dataset and control sample batch
deseq2 interactions batch effect correction grouping variable
updated 5.6 years ago by 42k • written 5.6 years ago by ▴ 90
0
votes
4
replies
1.9k
views
DESeq2 lfcShrink with interactions
deseq2 lfcShrink interactions
updated 5.3 years ago by 42k • written 5.3 years ago by • 0
0
votes
1
reply
617
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 2.5 years ago by 42k • written 2.5 years ago by • 0
0
votes
2
replies
1.2k
views
R package for molecule interactions?
r package function interactions
8.5 years ago amyfm ▴ 10
0
votes
1
reply
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 42k • written 8.6 years ago by ▴ 20
0
votes
3
replies
1.9k
views
DESeq2: interaction controlling for genetic effects
deseq interactions
updated 9.4 years ago by 42k • written 9.4 years ago by ▴ 10
0
votes
3
replies
896
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
0
votes
2
replies
1.0k
views
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
votes
2
replies
1.7k
views
DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 6.7 years ago by 42k • written 6.7 years ago by ▴ 10
0
votes
2
replies
1.5k
views
stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
updated 6.5 years ago by 42k • written 8.5 years ago by ★ 1.5k
0
votes
1
reply
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
votes
2
replies
786
views
results() function and finding the difference of differences
interactions DESeq2
2.5 years ago Nayrouz • 0
44 results • Page 1 of 1
Recent ...
Replies
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks a lot Peter, We solved the problem, IT had implemented a policy of RAM usage that started a conflict with any RAM-hungry process, m…
Answer: meffil.snp.concordance by James W. MacDonald 65k
This support site is meant to help people with technical questions about Bioconductor packages. The `meffil` package is not Bioconductor, n…
Answer: minfi latest update for EPIC V2 chip by James W. MacDonald 65k
Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for `minfi` so it will now distinguish the…
Votes
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to WouterDeCoster ▴ 130
Scholar to Michael Love 42k
Popular Question to Malcolm Cook ★ 1.6k
Popular Question to priyanka.m • 0
Locations • All
Switzerland, 17 minutes ago
United States, 20 minutes ago
Norway, 46 minutes ago
United States, 49 minutes ago
United States, 52 minutes ago
Traffic: 673 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6