Showing : Interactions • reset
5
votes
11
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12k
views
DESeq2: with multiple factors and interaction terms won't show all effects
deseq2 multiple factor design contrast interactions
updated 10.9 years ago by 43k • written 10.9 years ago by ▴ 110
6
votes
8
replies
3.7k
views
Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 5.1 years ago by • 0 • written 8.2 years ago by ▴ 60
2
votes
8
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3.6k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
10.6 years ago shao ▴ 100
3
votes
7
replies
5.3k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 9.8 years ago by 53k • written 9.8 years ago by ▴ 90
3
votes
7
replies
3.5k
views
DESeq2 lfcShrink with interactions
deseq2 interactions logfoldchange
updated 8.5 years ago by 43k • written 8.5 years ago by ▴ 70
1
vote
7
replies
3.5k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
11.2 years ago pshannon ▴ 100
13
votes
6
replies
8.0k
views
DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
updated 10.0 years ago by 43k • written 10.0 years ago by ▴ 290
2
votes
6
replies
2.5k
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 9.8 years ago by 43k • written 9.8 years ago by ▴ 10
1
vote
5
replies
1.3k
views
Testing Interactions without an interaction term in the design formula
deseq2 interactions
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 30
0
votes
5
replies
1.9k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
0
votes
5
replies
1.8k
views
Splitting a dataset and control sample batch
deseq2 interactions batch effect correction grouping variable
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 110
1
vote
5
replies
4.3k
views
Contrast All Interaction Effects in DESeq2 in current version (1.10.1)
DESeq2 differential gene expression interactions
10.2 years ago marcus.stoiber • 0
2
votes
5
replies
6.3k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
10.0 years ago rclaire ▴ 20
2
votes
5
replies
2.5k
views
How to make sense of the fold change values in the interaction results object.
deseq2 logfoldchange interactions
updated 9.8 years ago by 43k • written 9.8 years ago by ▴ 30
3
votes
5
replies
5.1k
views
DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 9.5 years ago by 43k • written 9.5 years ago by ▴ 10
1
vote
5
replies
1.9k
views
Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
7.8 years ago David R ▴ 90
3
votes
4
replies
3.6k
views
RNAseq analysis using edgeR - specifying and testing full factorial 2x2x4 model, main effects and interactions.
edger multiple factor design interactions
updated 10.8 years ago by ★ 29k • written 10.8 years ago by • 0
5
votes
4
replies
2.0k
views
Differential expression analysis desgin
differential expression deseq2 edger interactions limma
updated 8.3 years ago by 53k • written 8.3 years ago by ▴ 10
0
votes
4
replies
2.9k
views
DESeq2 lfcShrink with interactions
deseq2 lfcShrink interactions
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
2
votes
4
replies
6.7k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
9.8 years ago dwzhang.wisc ▴ 20
0
votes
3
replies
1.6k
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
11
votes
3
replies
4.4k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 60
0
votes
3
replies
2.3k
views
DESeq2: interaction controlling for genetic effects
deseq interactions
updated 11.1 years ago by 43k • written 11.1 years ago by ▴ 10
0
votes
3
replies
1.6k
views
DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
3
votes
3
replies
1.6k
views
Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 5.3 years ago by 53k • written 5.3 years ago by ▴ 10
6
votes
3
replies
6.4k
views
Calculating contrasts for continuous variable anad interaction effect in Limma
limma design matrix design and contrast matrix continuous interactions
updated 10.3 years ago by ★ 29k • written 10.3 years ago by ▴ 20
2
votes
3
replies
1.6k
views
DeSEQ2 factor effect without interaction effect
DESeq2 Interactions
5.0 years ago cossardg ▴ 10
8
votes
3
replies
3.4k
views
[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
9.3 years ago lanhuong ▴ 20
2
votes
3
replies
12k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 5.0 years ago by ★ 4.0k • written 5.1 years ago by ▴ 30
1
vote
2
replies
2.0k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
5.0 years ago Dan ▴ 20
0
votes
2
replies
1.6k
views
R package for molecule interactions?
r package function interactions
10.2 years ago amyfm ▴ 10
0
votes
2
replies
2.1k
views
stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
updated 8.2 years ago by 43k • written 10.2 years ago by ★ 1.5k
0
votes
2
replies
2.3k
views
DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 8.4 years ago by 43k • written 8.4 years ago by ▴ 10
0
votes
2
replies
1.5k
views
Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq edgeR makecontrasts interactions
updated 7.6 years ago by ★ 29k • written 7.6 years ago by ▴ 90
0
votes
2
replies
1.6k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 4.2 years ago by ★ 1.4k • written 4.2 years ago by • 0
0
votes
2
replies
1.3k
views
results() function and finding the difference of differences
interactions DESeq2
4.2 years ago Nayrouz • 0
0
votes
1
reply
1.8k
views
Using Effect Coding or Orthogonal Coding instead of dummy coding in DESeq2?
deseq2 multiple factor design interactions orthogonal coding effect coding
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by ▴ 20
0
votes
1
reply
2.1k
views
DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2 design and contrast matrix interactions contrast
updated 10.3 years ago by 43k • written 10.3 years ago by ▴ 20
1
vote
1
reply
1.9k
views
Interaction of fixed effects in DESeq2
deseq2 interactions
updated 10.6 years ago by 43k • written 10.6 years ago by • 0
4
votes
1
reply
2.9k
views
Limma: Contrasts with interaction term
limma interactions continuous term multiple factor design
updated 8.9 years ago by ★ 29k • written 8.9 years ago by ▴ 10
1
vote
1
reply
1.1k
views
Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
1
reply
988
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
0
votes
1
reply
1.3k
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 7.6 years ago by 68k • written 7.6 years ago by • 0
1
vote
0
replies
2.5k
views
Job: Bioinformatics / Biostatistics in genetic interaction analysis
high-throughput screening interactions genetics jobs image analysis Job
10.8 years ago Bernd Fischer ▴ 550
44 results • Page 1 of 1
Recent ...
Replies
Comment: Upcoming Ensembl API and data access changes - new blog post available by Hugo Gruson • 0
Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…
Comment: Are individual-mouse-based statistics possible in CellChat? by LillianaVolkman99 • 0
thank you very much. https://www.biostars.org/p/9617271/
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
My apologies, I forgot that `design.group` is not included in the final matrix, because the baseline group effects are already captured by …
Answer: Bile acid analysis with limpa by Gordon Smyth 53k
I am not familiar with targeted HPLC-MS and I don't know what you mean by "peak areas". If it produces standard format mass spec data from …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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