Showing : multiple factor design • reset
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Multi-factor blocking in DiffBind
diffbind differential binding analysis multiple factor design
written 7.5 years ago by ▴ 30
0
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1
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871
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DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
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5
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Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
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5
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DESeq2 package : Error in checkFullRank(modelMatrix) while designing multi factor
DESeq2 multiple factor design design model design matrix rna-seq
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
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4
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1.6k
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DESeq2 multifactor formula design
deseq2 time series multiple factor design
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
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6
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1.3k
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Another Matrix is not full rank question, multi-factor design issues
deseq2 model matrix not full rank multiple factor design
updated 6.3 years ago by 68k • written 6.3 years ago by • 0
3
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2
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1.4k
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EdgeR - blocking for multiple factors at once - Errors
EdgeR multiple factor design blocked design
updated 6.4 years ago by ★ 28k • written 6.4 years ago by ▴ 10
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1
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942
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Multiple factor design for differential expression with DESeq2
deseq2 differential gene expression multiple factor design
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
2
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4
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1.3k
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DESeq2 design with multiple factors
rnaseq deseq2 multiple factor design
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
3
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DESEQ2 normalize data of population data
deseq2 multiple factor design
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
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4
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DESeq2 design model that considers 3 factors
deseq2 multiple factor design
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
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10
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2.6k
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Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
deseq2 sequencing ribosome profiling riboseq multiple factor design
updated 6.6 years ago by 43k • written 6.6 years ago by ▴ 10
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5
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DESeq2 Subsetting gives error in contrasts - can be applied only to factors with 2 or more levels
deseq2 multiple factor design contrast
6.8 years ago russell.stewart.j • 0
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4
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DESeq2 design formula - how to account for donor and /or sample?
deseq2 multiple factor design rna-seq
updated 6.9 years ago by ★ 1.4k • written 6.9 years ago by • 0
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4
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1.3k
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Interaction effect sizes from DEXseq
dexseq multiple factor design
updated 6.9 years ago by ★ 1.9k • written 6.9 years ago by ▴ 10
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1
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937
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DESeq2: Multifactor design working with example data but not with my data
deseq2 multiple factor design
updated 6.9 years ago by 43k • written 6.9 years ago by ▴ 10
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2
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1.2k
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DESeq account for using two different siRNA constructs to knockdown same gene
deseq2 design and contrast matrix multiple factor design design matrix
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
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5
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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
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4
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1.2k
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Deseq multifactor test design full rank error and how to determine one variable only effect.
deseq2 multiple factor design design matrix
7.1 years ago • updated 7.0 years ago jaime.alvarez.benayas • 0
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12
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DESeq2 multifactor design with interaction term
deseq2 multiple factor design interaction term
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
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3
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Is this procedure necessary in DESeq2 for my data
deseq2 multiple factor design nested design
7.2 years ago • updated 7.1 years ago michael.steffen ▴ 20
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3
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DESeq2 Model matrix not full rank error despite fully-crossed experimental design
deseq2 multiple factor design
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
1
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2
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1.7k
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DESeq2 design & model matrix not full rank - am I nesting correctly?
deseq2 model matrix experimental design multiple factor design
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
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3
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1.7k
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Deseq2: 3 factors design
deseq2 multiple factor design
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
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5
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Clarification regarding analysis with multi-factorial design
limma multiple factor design sva voom
7.3 years ago scanchi • 0
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5
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2.8k
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Constant High Padj Values
deseq2 differential gene expression multiple factor design padj
updated 7.3 years ago by 43k • written 7.3 years ago by • 0
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1
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1.6k
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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
1
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7
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5.0k
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deseq2 analysis with multiple factors and interaction terms
deseq2 multiple factor design differential analysis differential gene expression
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 10
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1.8k
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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
1
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3
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1.3k
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Matrix is not full rank with Multifactorial Experiment and Time course
deseq2 multiple factor design model.matrix time course
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
3
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7
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2.6k
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complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 7.4 years ago by ★ 28k • written 7.4 years ago by ★ 1.5k
4
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11
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5.3k
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edgeR cpm filter
edger independent filtering multiple factor design cpm
updated 7.4 years ago by 52k • written 7.4 years ago by • 0
0
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4
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1.3k
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Design for DESeq2
LRT deseq2 multiple factor design
7.5 years ago sally_b86 • 0
1
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3
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DESeq2 experimental design
deseq2 multiple factor design
updated 7.5 years ago by ▴ 690 • written 7.5 years ago by ▴ 10
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2
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Differential gene expression for multi-factorial experiment using edgeR
edger differential gene expression multiple factor design
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
6
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19
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Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 7.5 years ago by ▴ 690 • written 7.5 years ago by ▴ 50
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2.4k
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DESeq2 Design controlling for gender
deseq2 multiple factor design
updated 7.5 years ago by 43k • written 7.5 years ago by • 0
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7
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2.5k
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DESeq2 - experimental design with 2 variables
deseq2 multiple factor design
7.6 years ago Jane Merlevede ▴ 90
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1
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1.5k
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Analyze time course experiment with multiple samples from multiple animals with DESeq2
deseq2 multiple factor design multifactorial design multiple time points design and contrast matrix
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 30
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1.9k
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Testing for DE genes between samples of isolated cells, accounting for expression in whole tissue
limma rnaseq rna-seq model-matrix multiple factor design
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 10
2
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1.4k
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Difference between DESeq2 1.14 and 1.16
deseq2 version multiple factor design
updated 7.6 years ago by ▴ 690 • written 7.6 years ago by • 0
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7
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3 factor design formula 'Model Matrix not full rank'
deseq2 multiple factor design
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 70
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8
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4.5k
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DESeq2 for multiple comparisons over time
deseq multiple factor design
7.6 years ago ucheuna • 0
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1
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1.4k
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Filtering the readcounts
deseq2 multiple factor design
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
2
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1
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DEseq2 time-series before and after Infection
multiple factor design deseq2 timecourse
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
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1
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DEseq2 design with paired individuals at two timepoints, two groups and two responses
deseq2 multiple factor design multiple time points paired samples
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
2
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6
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1.6k
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Complicated paired multi factor design
deseq2 multiple factor design
7.9 years ago • updated 7.8 years ago Vladimir Krasikov ▴ 90
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3
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DESeq2 Multiple Variable Nested Design
deseq2 multiple factor design nested design interaction term
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
5
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4
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1.7k
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interpretation of edgeR multi factor conditions in GLM
edger multivariate multiple factor design glm
updated 7.9 years ago by ★ 7.9k • written 7.9 years ago by • 0
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7
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2.1k
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DESeq2 design question - Two group treatment differences accounting for response
deseq2 interaction model multiple factor design multifactorial design
8.0 years ago jhutchin • 0
50 results • Page 1 of 1
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Comment: Explannation for ROAST results by ATpoint ★ 4.7k
The `contrast = 2` in an intercept-less design test whether the expression in the 2nd group is not 0. You can easily solve this by using `~…
Comment: Explannation for ROAST results by Jay • 0
BTW, AP1 is a character, composed of gene entrez ID, so is HIF1, UPR, etc al. And the rownames of `expr.i` is also gene entrez ID.
Comment: DESEQ2 looking at main effects while controlling for a continuous variable by Lennie • 0
Thanks James for your help! Sorry I am still a bit confused about the numerical contrast. In your example of c(0,1,0,0,0), where you are …
Answer: Merging annotation with differential expression output by James W. MacDonald 68k
This is just a general R question that you should be able to easily answer by using Google. Or you could ask on stackoverflow or biostars, …
Answer: Annotation package for Manduca sexta by shepherl 4.1k
Yes through the AnnotationHub ``` > library(AnnotationHub) > ah = AnnotationHub() snapshotDate(): 2024-10-28 > query(ah, "Manduc…
Votes
Comment: Limma comparing gene expression between base line and one treatment
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
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