Showing : multifactorial design • reset
12
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20
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2.0k
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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 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 830
11
votes
16
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1.8k
views
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
limma multifactorial design diagnostic plots affymetrix microarrays
updated 8.6 years ago by 65k • written 8.6 years ago by ▴ 830
6
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9
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1.6k
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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 7.9 years ago by 50k • written 7.9 years ago by ▴ 80
4
votes
6
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1.6k
views
Multi-factorial design for patient-replicates from different time points (Deseq2)
deseq2 rnaseq timecourse multiple time points multifactorial design
updated 7.2 years ago by 41k • written 7.2 years ago by • 0
4
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3
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3.3k
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limma: model/contrast matrix for 2x3 factorial design
limma multifactorial design design and contrast matrix limma design matrix limma contrast matrix
updated 8.1 years ago by 50k • written 8.1 years ago by • 0
4
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4
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2.1k
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How to handle the change in resultsNames() for DESeq2 ?
deseq2 resultsnames multifactorial design
updated 7.9 years ago by 41k • written 7.9 years ago by ▴ 10
3
votes
3
replies
871
views
edgeR multifactorial analysis implementation with RNA-Seq data
edger multifactorial design multiple comparisons differential gene expression
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 830
3
votes
5
replies
4.3k
views
DESeq2 3-fatcor design and different interaction terms
deseq2 bioconductor rnaseq multifactorial design interactions
updated 7.7 years ago by 41k • written 7.8 years ago by ▴ 10
3
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4
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2.1k
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
2
votes
5
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3.2k
views
deseq2 multifactor timeseries help
deseq2 multifactorial design time course
updated 7.0 years ago by • 0 • written 7.0 years ago by ▴ 10
2
votes
10
replies
2.1k
views
Design matrix for unbalanced data
edgeR RNA-Seq design matrix multifactorial design
8.2 years ago Yogender Gowtham ▴ 20
2
votes
2
replies
843
views
Correct formulation of contrasts of interest regarding an RNA-Seq gene expression analysis with edgeR
rnaseq edger design and contrast matrix multifactorial design
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
2
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1
reply
1.6k
views
Main effects in multi-level experiment in limma
limma multifactorial design
updated 8.6 years ago by ★ 7.9k • written 8.6 years ago by ▴ 70
2
votes
17
replies
4.1k
views
Multi-factorial design in DEseq2: defining reduced model
deseq2 multifactorial design reduced model
7.3 years ago laianavarromartin ▴ 20
2
votes
6
replies
2.8k
views
Understanding and creating various comparisons with model.matrix in limma regarding microarrays
limma microarray multifactorial design duplicatecorrelation model.matrix
8.4 years ago Konstantinos Yeles ▴ 80
1
vote
5
replies
1.5k
views
Differential expression (DESeq2) miRNAseq on patient samples
deseq2 multifactorial design multiple time points
updated 7.0 years ago by 41k • written 7.0 years ago by • 0
1
vote
7
replies
5.5k
views
[DESeq2] Multi-factor designs
deseq2 multifactorial design
8.0 years ago ofonov ▴ 10
1
vote
1
reply
1.1k
views
DESeq2 analysis with multiple biological parameters
deseq2 dexseq multiple factor design multifactorial design
updated 8.1 years ago by 41k • written 8.1 years ago by ★ 1.5k
1
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3
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1.7k
views
Three factor model matrix, contrasts with interactions - DESeq2 / edgeR
deseq2 edgeR multifactorial design limma voom
updated 7.0 years ago by 41k • written 7.0 years ago by ▴ 150
0
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1
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1.1k
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DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 4.4 years ago by 41k • written 4.4 years ago by • 0
0
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1
reply
2.0k
views
Multifactorial design in DESeq2 - how to answer biological questions
deseq2 multifactorial design
updated 8.2 years ago by 41k • written 8.2 years ago by • 0
0
votes
1
reply
2.9k
views
DESeq2 releveling not changing resultsNames options
deseq2 relevel resultsNames multifactorial design
updated 8.2 years ago by 41k • written 8.2 years ago by ▴ 20
0
votes
2
replies
1.2k
views
DESeq2 1.6 Multifactorial Design: Covariates with more than two classes?
deseq2 multiple factor design multifactorial design
updated 7.7 years ago by 41k • written 7.7 years ago by • 0
0
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5
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3.7k
views
DESeq2 - how to build design for multiple paired samples before/after with 2 conditions? (non-crossover)
deseq2 multifactorial design paired samples biologicalreplicates
7.2 years ago jahorst • 0
0
votes
2
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1.2k
views
DESeq2 removing columns from model matrix implication
deseq2 multifactorial design paired test
updated 7.2 years ago by 41k • written 7.2 years ago by ▴ 10
0
votes
7
replies
1.8k
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
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
0
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2
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1.4k
views
DESeq2 multifactorialdesign contrasts
deseq2 rnaseq multifactorial design design and contrast matrix
updated 6.7 years ago by ▴ 680 • written 6.7 years ago by • 0
0
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3
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1.7k
views
Interpretation of the log fold change for a time course/factorial design analysis in limma
limma rnaseq multifactorial design multiple time points
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
0
votes
5
replies
1.1k
views
differential expression analysis of cell subtypes mixture
deseq2 edgeR design matrix multifactorial design
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ★ 1.5k
0
votes
3
replies
1.1k
views
DESeq2 multifactor design, interpreting interaction names
deseq2 interactions multifactorial design
updated 5.7 years ago by 41k • written 5.7 years ago by • 0
0
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1
reply
1.3k
views
Appropriate selection of DE list in limma before and after implementation of arrayWeights in conjuction with duplicateCorrelation functions
limma microarray multifactorial design duplicatecorrelation arrayweights
8.4 years ago svlachavas ▴ 830
32 results • Page 1 of 1
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Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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