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 9.8 years ago by 43k • written 9.8 years ago by ▴ 110
2
votes
3
replies
9.4k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 3.9 years ago by ★ 4.0k • written 4.0 years ago by ▴ 30
13
votes
6
replies
7.5k
views
DESeq2 multiple interaction terms 3-factor design
deseq2 deseq interactions multiple factor design
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 290
2
votes
4
replies
5.9k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.7 years ago dwzhang.wisc ▴ 20
2
votes
5
replies
5.9k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.9 years ago rclaire ▴ 20
6
votes
3
replies
5.8k
views
Calculating contrasts for continuous variable anad interaction effect in Limma
limma design matrix design and contrast matrix continuous interactions
updated 9.2 years ago by ★ 28k • written 9.2 years ago by ▴ 20
3
votes
7
replies
4.7k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 8.7 years ago by 52k • written 8.7 years ago by ▴ 90
3
votes
5
replies
4.6k
views
DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 8.3 years ago by 43k • written 8.4 years ago by ▴ 10
1
vote
5
replies
3.8k
views
Contrast All Interaction Effects in DESeq2 in current version (1.10.1)
DESeq2 differential gene expression interactions
9.1 years ago marcus.stoiber • 0
11
votes
3
replies
3.6k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 60
2
votes
8
replies
3.3k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
9.5 years ago shao ▴ 100
3
votes
4
replies
3.2k
views
RNAseq analysis using edgeR - specifying and testing full factorial 2x2x4 model, main effects and interactions.
edger multiple factor design interactions
updated 9.6 years ago by ★ 28k • written 9.6 years ago by • 0
8
votes
3
replies
3.0k
views
[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
8.2 years ago lanhuong ▴ 20
3
votes
7
replies
3.0k
views
DESeq2 lfcShrink with interactions
deseq2 interactions logfoldchange
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 70
6
votes
8
replies
3.0k
views
Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 4.0 years ago by • 0 • written 7.1 years ago by ▴ 60
1
vote
7
replies
3.0k
views
Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
shiny network interactions
10.1 years ago pshannon ▴ 100
4
votes
1
reply
2.6k
views
Limma: Contrasts with interaction term
limma interactions continuous term multiple factor design
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 10
0
votes
4
replies
2.2k
views
DESeq2 lfcShrink with interactions
deseq2 lfcShrink interactions
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
1
vote
0
replies
2.2k
views
Job: Bioinformatics / Biostatistics in genetic interaction analysis
high-throughput screening interactions genetics jobs image analysis Job
9.7 years ago Bernd Fischer ▴ 550
0
votes
3
replies
2.1k
views
DESeq2: interaction controlling for genetic effects
deseq interactions
updated 10.0 years ago by 43k • written 10.0 years ago by ▴ 10
2
votes
6
replies
2.0k
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 8.6 years ago by 43k • written 8.6 years ago by ▴ 10
2
votes
5
replies
2.0k
views
How to make sense of the fold change values in the interaction results object.
deseq2 logfoldchange interactions
updated 8.7 years ago by 43k • written 8.7 years ago by ▴ 30
0
votes
2
replies
1.9k
views
DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
0
votes
1
reply
1.8k
views
DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2 design and contrast matrix interactions contrast
updated 9.2 years ago by 43k • written 9.2 years ago by ▴ 20
0
votes
2
replies
1.7k
views
stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
updated 7.1 years ago by 43k • written 9.1 years ago by ★ 1.5k
1
vote
1
reply
1.7k
views
Interaction of fixed effects in DESeq2
deseq2 interactions
updated 9.5 years ago by 43k • written 9.5 years ago by • 0
5
votes
4
replies
1.6k
views
Differential expression analysis desgin
differential expression deseq2 edger interactions limma
updated 7.2 years ago by 52k • written 7.2 years ago by ▴ 10
1
vote
2
replies
1.6k
views
How to do limma on 3 factors with multiple levels (e.g 3-way anova) on microarray log values
interactions 3factors limma Microarray
3.8 years ago Dan ▴ 20
0
votes
5
replies
1.6k
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Using Effect Coding or Orthogonal Coding instead of dummy coding in DESeq2?
deseq2 multiple factor design interactions orthogonal coding effect coding
updated 7.0 years ago by ★ 3.0k • written 7.0 years ago by ▴ 20
1
vote
5
replies
1.5k
views
Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
6.7 years ago David R ▴ 90
0
votes
5
replies
1.5k
views
Splitting a dataset and control sample batch
deseq2 interactions batch effect correction grouping variable
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 110
0
votes
2
replies
1.3k
views
R package for molecule interactions?
r package function interactions
9.1 years ago amyfm ▴ 10
0
votes
3
replies
1.3k
views
DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
3
votes
3
replies
1.3k
views
Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 4.2 years ago by 52k • written 4.2 years ago by ▴ 10
0
votes
2
replies
1.2k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 3.1 years ago by ★ 1.4k • written 3.1 years ago by • 0
0
votes
3
replies
1.2k
views
Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
2
votes
3
replies
1.2k
views
DeSEQ2 factor effect without interaction effect
DESeq2 Interactions
3.9 years ago cossardg ▴ 10
0
votes
2
replies
1.1k
views
Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq edgeR makecontrasts interactions
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 90
0
votes
1
reply
1.1k
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 6.5 years ago by 67k • written 6.5 years ago by • 0
1
vote
5
replies
1.1k
views
Testing Interactions without an interaction term in the design formula
deseq2 interactions
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 30
0
votes
2
replies
976
views
results() function and finding the difference of differences
interactions DESeq2
3.1 years ago Nayrouz • 0
1
vote
1
reply
786
views
Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 23 months ago by 43k • written 23 months ago by • 0
0
votes
1
reply
772
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
44 results • Page 1 of 1
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Comment: miRTarRnaseq library by María Calvo • 0
Hello Mercedeh, excuse me for not explaining it adecuately, Im using the "Part3 - Identify significant miRNA mRNA relationships for 2 time …
Comment: Need new version : tx2gene.gencode.v47.csv by Guido Hooiveld ★ 4.1k
Assuming that you would like to import the results from `salmon`, it is highly recommended to now use `tximeta`. By doing so, all required …
Comment: Help using rtracklayer for gene ID extraction by Aichatou • 0
Hello, Please disregard the previous post. it's working now, i think. I am able to create the txdb object but I can't see all the other inf…
Comment: p value is 0, padj is 0 by Wirayatida • 0
Than you so much. My counts are 47,37 and 72 for mock. The treatment is 8153, 6723 and 8024.
Comment: p value is 0, padj is 0 by Wirayatida • 0
Thank you so much for your information. I understand it.
Votes
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
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