Showing : Interactions • reset
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 10.1 years ago by 43k • written 10.1 years ago by ▴ 110
6
votes
8
replies
3.2k
views
Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 4.2 years ago by • 0 • written 7.4 years ago by ▴ 60
2
votes
8
replies
3.3k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
9.8 years ago shao ▴ 100
3
votes
7
replies
4.8k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 9.0 years ago by 52k • written 9.0 years ago by ▴ 90
3
votes
7
replies
3.1k
views
DESeq2 lfcShrink with interactions
deseq2 interactions logfoldchange
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 70
1
vote
7
replies
3.1k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
10.4 years ago pshannon ▴ 100
13
votes
6
replies
7.6k
views
DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
updated 9.2 years ago by 43k • written 9.2 years ago by ▴ 290
2
votes
6
replies
2.1k
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 8.9 years ago by 43k • written 8.9 years ago by ▴ 10
1
vote
5
replies
1.1k
views
Testing Interactions without an interaction term in the design formula
deseq2 interactions
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 30
0
votes
5
replies
1.7k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 10
0
votes
5
replies
1.5k
views
Splitting a dataset and control sample batch
deseq2 interactions batch effect correction grouping variable
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 110
1
vote
5
replies
3.9k
views
Contrast All Interaction Effects in DESeq2 in current version (1.10.1)
DESeq2 differential gene expression interactions
9.4 years ago marcus.stoiber • 0
2
votes
5
replies
6.0k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
9.2 years ago • updated 9.1 years ago rclaire ▴ 20
2
votes
5
replies
2.1k
views
How to make sense of the fold change values in the interaction results object.
deseq2 logfoldchange interactions
updated 9.0 years ago by 43k • written 9.0 years ago by ▴ 30
3
votes
5
replies
4.7k
views
DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 10
1
vote
5
replies
1.6k
views
Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
7.0 years ago David R ▴ 90
3
votes
4
replies
3.3k
views
RNAseq analysis using edgeR - specifying and testing full factorial 2x2x4 model, main effects and interactions.
edger multiple factor design interactions
updated 9.9 years ago by ★ 28k • written 9.9 years ago by • 0
5
votes
4
replies
1.7k
views
Differential expression analysis desgin
differential expression deseq2 edger interactions limma
updated 7.5 years ago by 52k • written 7.5 years ago by ▴ 10
0
votes
4
replies
2.4k
views
DESeq2 lfcShrink with interactions
deseq2 lfcShrink interactions
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
2
votes
4
replies
6.2k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
9.0 years ago dwzhang.wisc ▴ 20
0
votes
3
replies
1.3k
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
11
votes
3
replies
3.9k
views
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
0
votes
3
replies
2.2k
views
DESeq2: interaction controlling for genetic effects
deseq interactions
updated 10.3 years ago by 43k • written 10.3 years ago by ▴ 10
0
votes
3
replies
1.4k
views
DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
3
votes
3
replies
1.4k
views
Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 4.5 years ago by 52k • written 4.5 years ago by ▴ 10
6
votes
3
replies
6.0k
views
Calculating contrasts for continuous variable anad interaction effect in Limma
limma design matrix design and contrast matrix continuous interactions
updated 9.4 years ago by ★ 28k • written 9.4 years ago by ▴ 20
2
votes
3
replies
1.3k
views
DeSEQ2 factor effect without interaction effect
DESeq2 Interactions
4.2 years ago cossardg ▴ 10
8
votes
3
replies
3.2k
views
[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
8.5 years ago lanhuong ▴ 20
2
votes
3
replies
10k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by ▴ 30
1
vote
2
replies
1.7k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
4.1 years ago Dan ▴ 20
0
votes
2
replies
1.4k
views
R package for molecule interactions?
r package function interactions
9.4 years ago amyfm ▴ 10
0
votes
2
replies
1.8k
views
stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
updated 7.4 years ago by 43k • written 9.4 years ago by ★ 1.5k
0
votes
2
replies
2.0k
views
DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq edgeR makecontrasts interactions
updated 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 90
0
votes
2
replies
1.3k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 3.4 years ago by ★ 1.4k • written 3.4 years ago by • 0
0
votes
2
replies
1.0k
views
results() function and finding the difference of differences
interactions DESeq2
3.4 years ago Nayrouz • 0
0
votes
1
reply
1.6k
views
Using Effect Coding or Orthogonal Coding instead of dummy coding in DESeq2?
deseq2 multiple factor design interactions orthogonal coding effect coding
updated 7.3 years ago by ★ 3.0k • written 7.3 years ago by ▴ 20
0
votes
1
reply
1.9k
views
DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2 design and contrast matrix interactions contrast
updated 9.5 years ago by 43k • written 9.5 years ago by ▴ 20
1
vote
1
reply
1.7k
views
Interaction of fixed effects in DESeq2
deseq2 interactions
updated 9.8 years ago by 43k • written 9.8 years ago by • 0
4
votes
1
reply
2.6k
views
Limma: Contrasts with interaction term
limma interactions continuous term multiple factor design
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 10
1
vote
1
reply
841
views
Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
votes
1
reply
829
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
votes
1
reply
1.1k
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
1
vote
0
replies
2.3k
views
Job: Bioinformatics / Biostatistics in genetic interaction analysis
high-throughput screening interactions genetics jobs image analysis Job
9.9 years ago Bernd Fischer ▴ 550
44 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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