Showing : multiple factor design • reset
6
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19
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3.6k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 6.6 years ago by ▴ 680 • written 6.6 years ago by ▴ 50
11
votes
14
replies
4.2k
views
Setting up the Design Matrix
rnaseq edgeR multiple factor design design matrix
8.3 years ago Yogender Gowtham ▴ 20
4
votes
13
replies
2.0k
views
differential expression analysis using deseq2
deseq2 multiple factor design
updated 8.3 years ago by 41k • written 8.3 years ago by • 0
1
vote
12
replies
3.7k
views
Limma-voom design for multifactorial RNA-seq experiment
limma voom multiple factor design limma voom
8.4 years ago oliver.selmoni • 0
5
votes
12
replies
2.0k
views
how to use edgeR analysis RNA-seq data which has four factors
edger design matrix comparing more than two groups multiple factor design
8.3 years ago • updated 8.1 years ago xiaoaozqd • 0
8
votes
12
replies
4.2k
views
Interaction models in limma and multiple factor assessement regarding microarray statistical inference
limma microarray interaction model multiple factor design makeContrasts
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 830
4
votes
12
replies
3.3k
views
DESeq2 RNAseq analysis with "matrix not full rank" error corrected.
deseq2 multiple factor design
8.2 years ago yifangt ▴ 20
0
votes
12
replies
2.4k
views
Grouping a multifactor design in DESeq2 and accouting for sex
deseq2 multiple factor design group
updated 7.6 years ago by 41k • written 7.6 years ago by ▴ 90
1
vote
12
replies
1.7k
views
DESeq2 multifactor design with interaction term
deseq2 multiple factor design interaction term
updated 6.1 years ago by 41k • written 6.1 years ago by • 0
5
votes
11
replies
2.1k
views
edgeR Multifactor Design - Baseline
edgeR multiple factor design
updated 9.1 years ago by 50k • written 9.2 years ago by • 0
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
4
votes
11
replies
4.6k
views
edgeR cpm filter
edger independent filtering multiple factor design cpm
updated 6.5 years ago by 50k • written 6.5 years ago by • 0
2
votes
10
replies
4.7k
views
DESeqDataSet 2 factors with a covariate
covariate deseqdataset Deseq2 multiple factor design
updated 8.8 years ago by 41k • written 8.8 years ago by ▴ 10
1
vote
10
replies
2.1k
views
Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
deseq2 sequencing ribosome profiling riboseq multiple factor design
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 10
10
votes
9
replies
3.9k
views
EdgeR Multifactorial design with batch effect-trouble with defining contrasts
edger design and contrast matrix multiple factor design multiple comparisons
updated 8.8 years ago by 65k • written 8.8 years ago by ▴ 20
3
votes
8
replies
1.2k
views
DESEQ2 normalize data of population data
deseq2 multiple factor design
updated 5.6 years ago by 41k • written 5.6 years ago by • 0
0
votes
8
replies
4.0k
views
DESeq2 for multiple comparisons over time
deseq multiple factor design
6.7 years ago ucheuna • 0
0
votes
7
replies
2.2k
views
DESeq2 - experimental design with 2 variables
deseq2 multiple factor design
6.7 years ago Jane Merlevede ▴ 90
2
votes
7
replies
2.1k
views
3 factor design formula 'Model Matrix not full rank'
deseq2 multiple factor design
updated 6.7 years ago by 41k • written 6.7 years ago by ▴ 70
6
votes
7
replies
7.2k
views
EdgeR: glmLRT(), Multifactorial designs and correction for multiple testing
edgeR glmLRT() multiple factor design multiple testing correction
updated 9.3 years ago by ★ 28k • written 9.3 years ago by ▴ 80
3
votes
7
replies
2.0k
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ★ 1.5k
5
votes
7
replies
4.2k
views
edgeR design matrix
edger multiple factor design
8.9 years ago dongamit123 ▴ 20
1
vote
7
replies
4.1k
views
deseq2 analysis with multiple factors and interaction terms
deseq2 multiple factor design differential analysis differential gene expression
updated 6.4 years ago by 41k • written 6.4 years ago by ▴ 10
0
votes
7
replies
1.7k
views
DESeq2 design question - Two group treatment differences accounting for response
deseq2 interaction model multiple factor design multifactorial design
7.1 years ago jhutchin • 0
4
votes
7
replies
3.3k
views
Correct implementation of multifactorial paired analysis in limma software package for DE expression
limma microarray multiple factor design paired
updated 9.2 years ago by 50k • written 9.2 years ago by ▴ 830
2
votes
6
replies
1.2k
views
DESeq2 setup -- regular/interaction effect with two variables + replicates -- non-standard case
deseq2 multiple factor design
8.6 years ago Victor Missirian • 0
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
3
votes
6
replies
1.1k
views
Paired RNA-seq experiment with 3 factors using duplicateCorrelation
paired samples multiple factor design limma voom
updated 7.5 years ago by 50k • written 7.5 years ago by ▴ 90
11
votes
6
replies
3.7k
views
Log fold change on Limma
limma multiple factor design
updated 8.8 years ago by ★ 13k • written 8.8 years ago by ▴ 20
7
votes
6
replies
1.9k
views
edgeR (3.10.2) contrast question for experimental factors combined as a group
edgeR rnaseq multiple factor design
updated 8.9 years ago by ★ 7.9k • written 8.9 years ago by • 0
2
votes
6
replies
1.4k
views
Complicated paired multi factor design
deseq2 multiple factor design
7.0 years ago • updated 6.9 years ago Vladimir Krasikov ▴ 90
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
12
votes
6
replies
21k
views
DESEq2 comparison with mulitple cell types under 2 conditions
deseq2 multiple factor design
updated 9.0 years ago by 41k • written 9.0 years ago by ▴ 50
0
votes
6
replies
1.7k
views
DESeq2 design model-mothers & offspring timepoint comparisons
model.matrix multiple factor design design and contrast matrix deseq2
updated 8.7 years ago by 41k • written 8.7 years ago by • 0
0
votes
6
replies
979
views
Another Matrix is not full rank question, multi-factor design issues
deseq2 model matrix not full rank multiple factor design
updated 5.4 years ago by 65k • written 5.4 years ago by • 0
2
votes
5
replies
1.6k
views
DESeq2 problem with outlier replacement in paired multi-factor design
deseq2 differential gene expression multiple factor design paired design
7.3 years ago gregory.l.stone ▴ 10
1
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5
replies
2.3k
views
Constant High Padj Values
deseq2 differential gene expression multiple factor design padj
updated 6.4 years ago by 41k • written 6.4 years ago by • 0
0
votes
5
replies
1.7k
views
DESeq2 package : Error in checkFullRank(modelMatrix) while designing multi factor
DESeq2 multiple factor design design model design matrix rna-seq
updated 5.4 years ago by 41k • written 5.4 years ago by • 0
1
vote
5
replies
1.4k
views
Timecourse gene expression analysis with DESeq2
timecourse deseq2 multiple factor design LRT
updated 5.4 years ago by 41k • written 5.4 years ago by • 0
0
votes
5
replies
1.2k
views
Clarification regarding analysis with multi-factorial design
limma multiple factor design sva voom
6.4 years ago scanchi • 0
1
vote
5
replies
2.4k
views
DESeq2 Subsetting gives error in contrasts - can be applied only to factors with 2 or more levels
deseq2 multiple factor design contrast
5.9 years ago russell.stewart.j • 0
1
vote
5
replies
3.0k
views
Multifactor nested design in DESeq2 with non-paired data
DESeq2 multiple factor design
updated 8.3 years ago by 41k • written 8.3 years ago by • 0
4
votes
5
replies
1.8k
views
Multi-factor blocking in DiffBind
diffbind differential binding analysis multiple factor design
written 6.6 years ago by ▴ 30
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
0
votes
4
replies
1.7k
views
DESeq2 design matrix for normal & enriched samples
deseq2 multiple factor design
updated 9.0 years ago by 41k • written 9.0 years ago by • 0
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 9.0 years ago by ★ 28k • written 9.0 years ago by • 0
5
votes
4
replies
1.5k
views
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 6.7 years ago by ★ 28k • written 6.7 years ago by ▴ 10
2
votes
4
replies
924
views
Multi-level RNAseq experimental design question
limma multiple factor design
updated 8.8 years ago by ★ 28k • written 8.8 years ago by • 0
0
votes
4
replies
1.1k
views
Design for DESeq2
LRT deseq2 multiple factor design
6.6 years ago sally_b86 • 0
1
vote
4
replies
4.3k
views
Running DESeqDataSet with 4 factors?
summarizedexperiment deseq2 deseqdataset multiple factor design differential gene expression
8.8 years ago Lillyhchen ▴ 10
50 results • Page 1 of 1
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Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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