Showing : multifactorial design • reset
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DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 4.0 years ago by 41k • written 4.0 years ago by • 0
2
votes
2
replies
715
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Correct formulation of contrasts of interest regarding an RNA-Seq gene expression analysis with edgeR
rnaseq edger design and contrast matrix multifactorial design
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
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3
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1.0k
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DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
0
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5
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965
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differential expression analysis of cell subtypes mixture
deseq2 edgeR design matrix multifactorial design
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ★ 1.5k
3
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3
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744
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edgeR multifactorial analysis implementation with RNA-Seq data
edger multifactorial design multiple comparisons differential gene expression
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 820
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3
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1.5k
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Interpretation of the log fold change for a time course/factorial design analysis in limma
limma rnaseq multifactorial design multiple time points
updated 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
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1
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1.2k
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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 6.3 years ago by 41k • written 6.3 years ago by ▴ 30
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2
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1.3k
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DESeq2 multifactorialdesign contrasts
deseq2 rnaseq multifactorial design design and contrast matrix
updated 6.3 years ago by ▴ 670 • written 6.3 years ago by • 0
1
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3
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1.6k
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Three factor model matrix, contrasts with interactions - DESeq2 / edgeR
deseq2 edgeR multifactorial design limma voom
updated 6.5 years ago by 41k • written 6.6 years ago by ▴ 150
2
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5
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3.0k
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deseq2 multifactor timeseries help
deseq2 multifactorial design time course
updated 6.6 years ago by • 0 • written 6.6 years ago by ▴ 10
1
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5
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1.4k
views
Differential expression (DESeq2) miRNAseq on patient samples
deseq2 multifactorial design multiple time points
updated 6.6 years ago by 41k • written 6.6 years ago by • 0
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7
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1.6k
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DESeq2 design question - Two group treatment differences accounting for response
deseq2 interaction model multiple factor design multifactorial design
6.7 years ago jhutchin • 0
4
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6
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1.4k
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Multi-factorial design for patient-replicates from different time points (Deseq2)
deseq2 rnaseq timecourse multiple time points multifactorial design
updated 6.7 years ago by 41k • written 6.8 years ago by • 0
0
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5
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3.5k
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DESeq2 - how to build design for multiple paired samples before/after with 2 conditions? (non-crossover)
deseq2 multifactorial design paired samples biologicalreplicates
6.8 years ago jahorst • 0
0
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2
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1.1k
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DESeq2 removing columns from model matrix implication
deseq2 multifactorial design paired test
updated 6.8 years ago by 41k • written 6.8 years ago by ▴ 10
2
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17
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3.7k
views
Multi-factorial design in DEseq2: defining reduced model
deseq2 multifactorial design reduced model
6.8 years ago laianavarromartin ▴ 20
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4
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1.8k
views
Deseq2 DE between WT and MUTANT normalised with respect to control
deseq2 multiple factor design design and contrast matrix design multifactorial design
7.2 years ago shimbalama • 0
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2
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1.1k
views
DESeq2 1.6 Multifactorial Design: Covariates with more than two classes?
deseq2 multiple factor design multifactorial design
updated 7.3 years ago by 41k • written 7.3 years ago by • 0
3
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5
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4.2k
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DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 7.3 years ago by 41k • written 7.3 years ago by ▴ 10
6
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9
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1.4k
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Interpretation of DE analysis results of an Illumina microarray dataset, and possible batch effect size problem
limma illumina microarray multifactorial design batch effect
updated 7.4 years ago by 48k • written 7.4 years ago by ▴ 80
4
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4
replies
1.9k
views
How to handle the change in resultsNames() for DESeq2 ?
deseq2 resultsnames multifactorial design
updated 7.5 years ago by 41k • written 7.5 years ago by ▴ 10
1
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7
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5.4k
views
[DESeq2] Multi-factor designs
deseq2 multifactorial design
7.6 years ago ofonov ▴ 10
4
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3
replies
3.1k
views
limma: model/contrast matrix for 2x3 factorial design
limma multifactorial design design and contrast matrix limma design matrix limma contrast matrix
updated 7.6 years ago by 48k • written 7.6 years ago by • 0
1
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1
reply
1.0k
views
DESeq2 analysis with multiple biological parameters
deseq2 dexseq multiple factor design multifactorial design
updated 7.7 years ago by 41k • written 7.7 years ago by ★ 1.5k
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1
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2.7k
views
DESeq2 releveling not changing resultsNames options
deseq2 relevel resultsNames multifactorial design
updated 7.7 years ago by 41k • written 7.7 years ago by ▴ 20
2
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10
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1.8k
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Design matrix for unbalanced data
edgeR RNA-Seq design matrix multifactorial design
7.8 years ago Yogender Gowtham ▴ 20
0
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1
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1.9k
views
Multifactorial design in DESeq2 - how to answer biological questions
deseq2 multifactorial design
updated 7.8 years ago by 41k • written 7.8 years ago by • 0
2
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6
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2.6k
views
Understanding and creating various comparisons with model.matrix in limma regarding microarrays
limma microarray multifactorial design duplicatecorrelation model.matrix
7.9 years ago Konstantinos Yeles ▴ 80
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1
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1.2k
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Appropriate selection of DE list in limma before and after implementation of arrayWeights in conjuction with duplicateCorrelation functions
limma microarray multifactorial design duplicatecorrelation arrayweights
8.0 years ago svlachavas ▴ 820
2
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1
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1.5k
views
Main effects in multi-level experiment in limma
limma multifactorial design
updated 8.1 years ago by 7.8k • written 8.2 years ago by ▴ 70
11
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16
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1.6k
views
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
limma multifactorial design diagnostic plots affymetrix microarrays
updated 8.2 years ago by 64k • written 8.2 years ago by ▴ 820
12
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20
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1.9k
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Possible implementation of multifactorial contrasts in limma regarding a microarray dataset
limma multifactorial design design and contrast matrix affymetrix microarrays
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 820
32 results • Page 1 of 1
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Replies
Comment: Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and by Aastha Kapoor • 0
After several attempts the code has worked. I connected to a faster internet connection. set the timeout (1000000) and run the command. I …
Comment: DESeq2 estimateSizeFactors iterate takes too long by Karthik • 0
Hello, I agree with you, and we are in process of working with collaborators, but I wanted to get a general opinion on the data and get a …
Comment: It's possible to use clusterProfiler without an annotationDBI package by Guido Hooiveld ★ 3.8k
Code to show it works: > library(clusterProfiler) > > ## use provided 10 IDs, plus as last one add ID that has a GO annotati…
Comment: It's possible to use clusterProfiler without an annotationDBI package by Guido Hooiveld ★ 3.8k
You are almost there... Yet - pay attention to the error message (`--> No gene can be mapped.... --> Expected input gene ID: GO:0055080, .…
Comment: Problem loading HDF5Array in R 4.3.2 by Sarah • 0
Thanks for the reply! I tried this and it is crashing at `h5createFile("test.h5")` even after reinstalling **Rhdf5lib** and **rhdf5** It …
Votes
Answer: Limma/DESeq2 for unbalanced nested design (paired samples)
Result from GSEA for non-model organism not as expected
Comment: DESeq2 estimateSizeFactors iterate takes too long
Answer: DESeq2 estimateSizeFactors iterate takes too long
Comment: biomaRtl returns multiple GO terms when filtering on a single GO term in ensembl
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