Showing : multiple factor design • reset
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
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
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
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
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
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
6
votes
19
replies
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
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
6
votes
1
reply
2.5k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 8.4 years ago by 41k • written 8.4 years ago by ▴ 60
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
5
votes
4
replies
1.4k
views
interpretation of edgeR multi factor conditions in GLM
edger multivariate multiple factor design glm
updated 7.0 years ago by ★ 7.9k • written 7.0 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 9.1 years ago by • 0
5
votes
4
replies
7.4k
views
edgeR cpm filter with >1 factor
edger cpm multiple factor design independent filtering
8.3 years ago dietahanson ▴ 30
5
votes
7
replies
4.2k
views
edgeR design matrix
edger multiple factor design
8.9 years ago dongamit123 ▴ 20
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
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
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
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
4
votes
13
replies
2.0k
views
differential expression analysis using deseq2
deseq2 multiple factor design
updated 8.2 years ago by 41k • written 8.3 years ago by • 0
4
votes
3
replies
2.9k
views
DESeq2 - design for TCGA level 3 data
deseq2 tcga experimental design multiple factor design
updated 8.9 years ago by 41k • written 8.9 years ago by ▴ 40
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
4
votes
2
replies
1.2k
views
Differential gene expression for multi-factorial experiment using edgeR
edger differential gene expression multiple factor design
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
4
votes
4
replies
1.8k
views
Deseq2 results interpretation
deseq2 multiple factor design results
7.9 years ago koeniger ▴ 10
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
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
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
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
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
3
votes
3
replies
10k
views
DESeq2: multiple factors and comparison of a main factor between samples
deseq2 multiple factor design
updated 9.1 years ago by 41k • written 9.1 years ago by ▴ 90
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
3
votes
4
replies
2.0k
views
Deseq2 DE between WT and MUTANT normalised with respect to control
deseq2 multiple factor design design and contrast matrix design multifactorial design
7.6 years ago shimbalama • 0
3
votes
2
replies
2.1k
views
DESEQ2 (R) design/contrast formula questions
deseq2 phyloseq multiple factor design paired samples
updated 8.1 years ago by ▴ 20 • written 8.1 years ago by ▴ 10
3
votes
4
replies
1.5k
views
Appropriate design matrix set up in limma for 2-factor approches with NA values for specific levels
limma multiple factor design NA values design and contrast matrix
updated 7.2 years ago by 50k • written 7.2 years ago by ▴ 830
3
votes
2
replies
1.1k
views
EdgeR - blocking for multiple factors at once - Errors
EdgeR multiple factor design blocked design
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 10
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
2
replies
2.6k
views
Correct creation of design matrix in limma regarding a multi-level experiment
limma multiple factor design affymetrix microarrays limma paired analysis
updated 8.7 years ago by 50k • written 8.7 years ago by ▴ 830
2
votes
2
replies
1.9k
views
edgeR: experiments with multiple factors comparisons
limma multiple factor design multiple comparisons
updated 7.6 years ago by 50k • written 7.6 years ago by • 0
2
votes
10
replies
4.7k
views
DESeqDataSet 2 factors with a covariate
covariate deseqdataset Deseq2 multiple factor design
updated 8.7 years ago by 41k • written 8.7 years ago by ▴ 10
2
votes
4
replies
923
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
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
3
replies
2.9k
views
Help with DESeq2 Multiple Factor Design
deseq2 design multiple factor design
updated 9.1 years ago by ▴ 610 • written 9.1 years ago by • 0
2
votes
4
replies
1.0k
views
DESeq2 design with multiple factors
rnaseq deseq2 multiple factor design
updated 5.5 years ago by 41k • written 5.6 years ago by • 0
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
2
votes
1
reply
1.2k
views
Difference between DESeq2 1.14 and 1.16
deseq2 version multiple factor design
updated 6.7 years ago by ▴ 680 • written 6.7 years ago by • 0
2
votes
1
reply
1.6k
views
design and annotation question using DESeq2
deseq2 annotation multiple factor design
updated 8.9 years ago by 41k • written 8.9 years ago by ▴ 10
2
votes
1
reply
1.0k
views
DEseq2 time-series before and after Infection
multiple factor design deseq2 timecourse
updated 6.8 years ago by 41k • written 6.8 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
2
votes
3
replies
2.8k
views
Questions in limma about multifactorial design and possible batch effect correction
limma batcheffect batcheffectcorrection multiple factor design
updated 9.0 years ago by 65k • written 9.0 years ago by ▴ 830
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
50 results • Page 1 of 1
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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…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
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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