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 9.2 years ago by 42k • written 9.2 years ago by ▴ 90
6
votes
8
replies
2.5k
views
Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 3.4 years ago by • 0 • written 6.6 years ago by ▴ 60
2
votes
8
replies
3.1k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
8.9 years ago shao ▴ 100
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
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
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
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
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 8.1 years ago by 42k • written 8.1 years ago by ▴ 10
1
vote
5
replies
868
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
0
votes
5
replies
1.4k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 5.7 years ago by 42k • written 5.7 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
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
2
votes
5
replies
5.5k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.3 years ago rclaire ▴ 20
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
3
votes
5
replies
4.4k
views
DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 7.8 years ago by 42k • written 7.8 years ago by ▴ 10
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
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 9.1 years ago by ★ 28k • written 9.1 years ago by • 0
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
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
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
0
votes
3
replies
914
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
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
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
1.1k
views
DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 5.8 years ago by 42k • written 5.8 years ago by • 0
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
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
2
votes
3
replies
1.0k
views
DeSEQ2 factor effect without interaction effect
DESeq2 Interactions
3.3 years ago cossardg ▴ 10
8
votes
3
replies
2.7k
views
[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
7.7 years ago lanhuong ▴ 20
2
votes
3
replies
7.6k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 3.4 years ago by ★ 3.9k • written 3.4 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
3.3 years ago Dan ▴ 20
0
votes
2
replies
1.2k
views
R package for molecule interactions?
r package function interactions
8.5 years ago amyfm ▴ 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
2
replies
1.7k
views
DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 6.8 years ago by 42k • written 6.8 years ago by ▴ 10
0
votes
2
replies
936
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
2
replies
1.0k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 2.5 years ago by ★ 1.4k • written 2.5 years ago by • 0
0
votes
2
replies
791
views
results() function and finding the difference of differences
interactions DESeq2
2.6 years ago Nayrouz • 0
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 6.5 years ago by ★ 3.0k • written 6.5 years ago by ▴ 20
0
votes
1
reply
1.7k
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
1
vote
1
reply
1.5k
views
Interaction of fixed effects in DESeq2
deseq2 interactions
updated 9.0 years ago by 42k • written 9.0 years ago by • 0
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
1
vote
1
reply
637
views
Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 16 months ago by 42k • written 16 months ago by • 0
0
votes
1
reply
625
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
1
reply
957
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
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
44 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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