Showing : interactions • reset
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626
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Is this DESeq2 interactions design correct?
DESeq2 interactions
updated 15 months ago by 41k • written 15 months ago by • 0
0
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2
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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
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1
reply
614
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Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 2.5 years ago by 41k • written 2.5 years ago by • 0
0
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2
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781
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results() function and finding the difference of differences
interactions DESeq2
2.5 years ago Nayrouz • 0
0
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3
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887
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Analysis of interactions in RNAseq data: LRT vs 2 way ANOVA
DESeq2 LRT two-way-ANOVA interactions
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
1
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2
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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
2
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3
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1.0k
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DeSEQ2 factor effect without interaction effect
DESeq2 Interactions
3.3 years ago cossardg ▴ 10
2
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3
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7.4k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by ▴ 30
6
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8
replies
2.4k
views
Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 3.3 years ago by • 0 • written 6.5 years ago by ▴ 60
3
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3
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1.1k
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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
1
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5
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864
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Testing Interactions without an interaction term in the design formula
deseq2 interactions
updated 5.1 years ago by 41k • written 5.1 years ago by ▴ 30
0
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4
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1.9k
views
DESeq2 lfcShrink with interactions
deseq2 lfcShrink interactions
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
0
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5
replies
1.2k
views
Splitting a dataset and control sample batch
deseq2 interactions batch effect correction grouping variable
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 90
0
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5
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1.4k
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RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 10
0
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3
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1.1k
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DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 5.7 years ago by 41k • written 5.7 years ago by • 0
0
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2
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931
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Circumventing statistical non-significance on a triple interaction using edgeR
rnaseq edgeR makecontrasts interactions
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 90
0
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1
reply
950
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
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5
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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
0
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1
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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
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2
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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 41k • written 8.5 years ago by ★ 1.5k
8
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3
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3.0k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 6.6 years ago by 41k • written 6.6 years ago by ▴ 50
5
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4
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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
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2
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1.6k
views
DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 6.7 years ago by 41k • written 6.7 years ago by ▴ 10
3
votes
7
replies
2.8k
views
DESeq2 lfcShrink with interactions
deseq2 interactions logfoldchange
updated 6.8 years ago by 41k • written 6.8 years ago by ▴ 70
4
votes
1
reply
2.4k
views
Limma: Contrasts with interaction term
limma interactions continuous term multiple factor design
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 10
8
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3
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2.7k
views
[Limma] Testing continuous variable with interaction
limma voom continuous interactions confounding
7.6 years ago lanhuong ▴ 20
3
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5
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4.3k
views
DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 7.7 years ago by 41k • written 7.7 years ago by ▴ 10
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 41k • written 8.0 years ago by ▴ 10
2
votes
4
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5.4k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
8.1 years ago dwzhang.wisc ▴ 20
3
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7
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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
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 41k • written 8.1 years ago by ▴ 30
2
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5
replies
5.5k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
8.3 years ago • updated 8.2 years ago rclaire ▴ 20
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 41k • written 8.3 years ago by ▴ 290
1
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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
0
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2
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1.2k
views
R package for molecule interactions?
r package function interactions
8.5 years ago amyfm ▴ 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 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 20
0
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1
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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 41k • written 8.6 years ago by ▴ 20
2
votes
8
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3.1k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
8.9 years ago shao ▴ 100
1
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1
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1.5k
views
Interaction of fixed effects in DESeq2
deseq2 interactions
updated 8.9 years ago by 41k • written 8.9 years ago by • 0
3
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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
1
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0
replies
2.0k
views
Job: Bioinformatics / Biostatistics in genetic interaction analysis
high-throughput screening interactions genetics jobs image analysis Job
9.0 years ago Bernd Fischer ▴ 550
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 41k • written 9.2 years ago by ▴ 90
0
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3
replies
1.9k
views
DESeq2: interaction controlling for genetic effects
deseq interactions
updated 9.4 years ago by 41k • written 9.4 years ago by ▴ 10
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
44 results • Page 1 of 1
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Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Comment: Store output of matchPWM() by James W. MacDonald 65k
Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…
Comment: DEseq2 coefficient by JKim • 0
Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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