Showing : multiple factor design • reset
4
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5
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1.8k
views
Multi-factor blocking in DiffBind
diffbind differential binding analysis multiple factor design
written 6.6 years ago by ▴ 30
0
votes
1
reply
676
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
1
vote
5
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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
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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
0
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4
replies
1.2k
views
DESeq2 multifactor formula design
deseq2 time series multiple factor design
updated 5.4 years ago by 41k • written 5.4 years ago by • 0
0
votes
6
replies
977
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
3
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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
0
votes
1
reply
767
views
Multiple factor design for differential expression with DESeq2
deseq2 differential gene expression multiple factor design
updated 5.5 years ago by 41k • written 5.5 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 5.5 years ago by • 0
3
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8
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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
1
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4
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1.5k
views
DESeq2 design model that considers 3 factors
deseq2 multiple factor design
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 10
1
vote
10
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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
1
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5
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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
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4
replies
1.6k
views
DESeq2 design formula - how to account for donor and /or sample?
deseq2 multiple factor design rna-seq
updated 6.0 years ago by ★ 1.3k • written 6.0 years ago by • 0
0
votes
4
replies
1.0k
views
Interaction effect sizes from DEXseq
dexseq multiple factor design
updated 6.0 years ago by ★ 1.9k • written 6.0 years ago by ▴ 10
0
votes
1
reply
763
views
DESeq2: Multifactor design working with example data but not with my data
deseq2 multiple factor design
updated 6.0 years ago by 41k • written 6.0 years ago by ▴ 10
0
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2
replies
1.0k
views
DESeq account for using two different siRNA constructs to knockdown same gene
deseq2 design and contrast matrix multiple factor design design matrix
updated 6.0 years ago by 41k • written 6.0 years ago by • 0
1
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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 • updated 6.0 years ago David R ▴ 90
1
vote
4
replies
939
views
Deseq multifactor test design full rank error and how to determine one variable only effect.
deseq2 multiple factor design design matrix
6.1 years ago jaime.alvarez.benayas • 0
1
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12
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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
0
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3
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968
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Is this procedure necessary in DESeq2 for my data
deseq2 multiple factor design nested design
6.2 years ago michael.steffen ▴ 20
0
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3
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1.1k
views
DESeq2 Model matrix not full rank error despite fully-crossed experimental design
deseq2 multiple factor design
updated 6.3 years ago by 41k • written 6.3 years ago by • 0
1
vote
2
replies
1.4k
views
DESeq2 design & model matrix not full rank - am I nesting correctly?
deseq2 model matrix experimental design multiple factor design
updated 6.3 years ago by 41k • written 6.3 years ago by • 0
0
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3
replies
1.5k
views
Deseq2: 3 factors design
deseq2 multiple factor design
updated 6.4 years ago by 41k • written 6.4 years ago by • 0
0
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5
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1.2k
views
Clarification regarding analysis with multi-factorial design
limma multiple factor design sva voom
6.4 years ago scanchi • 0
1
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5
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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
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1
reply
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
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
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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 8.4 years ago by ★ 1.5k
1
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3
replies
1.1k
views
Matrix is not full rank with Multifactorial Experiment and Time course
deseq2 multiple factor design model.matrix time course
updated 6.5 years ago by 41k • written 6.5 years ago by • 0
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
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
0
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4
replies
1.1k
views
Design for DESeq2
LRT deseq2 multiple factor design
6.6 years ago sally_b86 • 0
1
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3
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2.0k
views
DESeq2 experimental design
deseq2 multiple factor design
updated 6.6 years ago by ▴ 680 • written 6.6 years ago by ▴ 10
4
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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
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
0
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1
reply
2.1k
views
DESeq2 Design controlling for gender
deseq2 multiple factor design
updated 6.6 years ago by 41k • written 6.6 years ago by • 0
0
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7
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2.2k
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DESeq2 - experimental design with 2 variables
deseq2 multiple factor design
6.7 years ago Jane Merlevede ▴ 90
0
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1
reply
1.3k
views
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 6.7 years ago by 41k • written 6.7 years ago by ▴ 30
5
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4
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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
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
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7
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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
0
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8
replies
4.0k
views
DESeq2 for multiple comparisons over time
deseq multiple factor design
6.7 years ago ucheuna • 0
0
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1
reply
1.2k
views
Filtering the readcounts
deseq2 multiple factor design
updated 6.7 years ago by 41k • written 6.7 years ago by • 0
2
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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
0
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1
reply
1.8k
views
DEseq2 design with paired individuals at two timepoints, two groups and two responses
deseq2 multiple factor design multiple time points paired samples
updated 6.8 years ago by 41k • written 6.8 years ago by • 0
2
votes
6
replies
1.4k
views
Complicated paired multi factor design
deseq2 multiple factor design
6.9 years ago Vladimir Krasikov ▴ 90
0
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3
replies
4.5k
views
DESeq2 Multiple Variable Nested Design
deseq2 multiple factor design nested design interaction term
updated 6.9 years ago by 41k • written 7.0 years ago by • 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
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
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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