Showing : Design matrix • reset
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DESeq2 accounting for two confounders with interaction in the design matrix
deseq2 design matrix multi-confounders linear models rna-seq
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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2
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1.2k
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Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2 design formula design matrix edgeR ATAC
updated 5.9 years ago by 53k • written 5.9 years ago by • 0
1
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4
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2.4k
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edgeR design matrix for 2 variables + batch effect
egdeR design matrix batch effect
updated 6.0 years ago by 53k • written 6.0 years ago by • 0
0
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2
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979
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DESeq2 design matrix choice
deseq2 design matrix
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
2
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1
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1.5k
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Limma Design matrix for time series+treatment+batch effect
limma factorial design matrix microarray
updated 6.3 years ago by ★ 29k • written 6.3 years ago by • 0
1
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5
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1.4k
views
DESEQ2 design matrix for double knockout interaction with condition
deseq2 model.matrix design matrix
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
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1
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1.1k
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DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 6.5 years ago by 43k • written 6.5 years ago by ▴ 30
0
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0
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997
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Paired DE analysis in edgeR with trios of samples while blocking for various confounders
edger rnaseq paired analysis design matrix
6.6 years ago svlachavas ▴ 840
2
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10
replies
4.0k
views
Time-series analysis with DESeq2
deseq2 time-series design matrix edger
updated 6.7 years ago by 43k • written 6.7 years ago by ★ 1.5k
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1
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1.1k
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differentail expression analysis with interaction terms
edger deseq2 interaction design matrix
updated 6.8 years ago by 68k • written 6.8 years ago by ★ 1.5k
2
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2
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1.3k
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Limma design matrix separate channel analysis with same control
limma design matrix gene expression
updated 6.8 years ago by 53k • written 6.8 years ago by • 0
4
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9
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1.8k
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Statistical background for computing intial estimates for the means of negative binomially distributed gene counts in DESeq2
deseq2 design matrix
6.9 years ago nikosbosse • 0
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5
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2.3k
views
DESeq2 package : Error in checkFullRank(modelMatrix) while designing multi factor
DESeq2 multiple factor design design model design matrix rna-seq
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
2
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2
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1.2k
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DESeq results gives all genes
deseq2 design matrix results
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
2
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1
reply
1.3k
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EdgeR: With two treatments, is it equivalent to split into two different models vs. making the relevant pairwise comparisons?
edgeR design matrix contrast
updated 7.0 years ago by 53k • written 7.0 years ago by • 0
2
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2
replies
1.8k
views
EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
edger design matrix glmlrt() glmQFTest() paired design
7.0 years ago oakhamwolf • 0
0
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1
reply
1.3k
views
Creating a design matrix
design matrix limma
updated 7.0 years ago by 53k • written 7.2 years ago by ▴ 20
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11
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5.2k
views
Limma Design Matrix for Paired Samples with Confouding Factors
limma design matrix paired samples confounding factors
updated 7.1 years ago by ★ 29k • written 7.1 years ago by • 0
5
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7
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4.6k
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Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 10
2
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1
reply
993
views
edgeR with related individuals?
edgeR related design matrix
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
5
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5
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2.1k
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Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma design and contrast matrix design matrix contrast matrix
updated 7.1 years ago by 68k • written 7.1 years ago by ▴ 280
2
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4
replies
3.1k
views
Design Matrix with paired and independent samples plus RUVg Spike-in normalization
edger design matrix paired samples ruvseq
updated 4 months ago by • 0 • written 7.3 years ago by • 0
3
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8
replies
1.9k
views
Design matrix for a two-color experimental design testing for time effect on 3 treated cell-lines, each with its own time=0 control
limma microarray design matrix twochannel
updated 7.3 years ago by 53k • written 7.3 years ago by ▴ 110
1
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8
replies
2.5k
views
Design matrix for regressing gene expression on a continuous variable - age
limma lmfit design matrix r
updated 7.3 years ago by ★ 29k • written 7.3 years ago by • 0
2
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10
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2.5k
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Am I on the right tracks with a 3 factor design in Limma?
r limma design matrix biobase
updated 7.4 years ago by 53k • written 7.4 years ago by • 0
0
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1
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1.8k
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Test for differential variability with missMethyl (DiffVar) using block design
missmethyl diffvar design matrix limma block
updated 7.5 years ago by ▴ 50 • written 8.4 years ago by ▴ 190
4
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4
replies
2.2k
views
edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression model.matrix design matrix
updated 7.5 years ago by 53k • written 7.5 years ago by • 0
3
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7
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2.3k
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single continuous factor
edger design matrix continuous
updated 3.8 years ago by • 0 • written 7.5 years ago by • 0
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2
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1.0k
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Limma design matrix
limma design matrix
updated 7.5 years ago by 53k • written 7.5 years ago by ▴ 40
0
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1
reply
981
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RNAseq DESeq2 paired data design help
rnaseq design matrix deseq2
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
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2
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9.4k
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DESEQ2 design with multiple conditions
deseq2 design matrix
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
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2
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1.4k
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DESeq account for using two different siRNA constructs to knockdown same gene
deseq2 design and contrast matrix multiple factor design design matrix
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
3
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6
replies
1.8k
views
EdgeR model formula design matrix
edger design matrix paired samples
updated 7.6 years ago by ★ 29k • written 7.6 years ago by • 0
0
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5
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1.7k
views
differential expression analysis of cell subtypes mixture
deseq2 edgeR design matrix multifactorial design
updated 7.7 years ago by ★ 29k • written 7.7 years ago by ★ 1.5k
0
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4
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2.3k
views
edgeR design matrix
edgeR design and contrast matrix design matrix
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 20
1
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4
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1.3k
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Deseq multifactor test design full rank error and how to determine one variable only effect.
deseq2 multiple factor design design matrix
7.7 years ago jaime.alvarez.benayas • 0
2
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13
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2.9k
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LIMMA : group specific effect of a treatment while controlling for individual effect
limma-voom design matrix limma time-course limma design matrix limma
7.7 years ago SPbeginner • 0
1
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18
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3.2k
views
Microarray expression analysis for on factor taking account confounders (covariables)
limma design matrix matrix with covariables
updated 7.7 years ago by ★ 29k • written 7.7 years ago by • 0
5
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2
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2.5k
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DESeq2 batch effect with and without interaction model
deseq2 rna-seq R linear model design matrix
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 10
0
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2
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2.0k
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stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
updated 8.0 years ago by 43k • written 10.0 years ago by ★ 1.5k
3
votes
7
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2.9k
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ★ 1.5k
6
votes
3
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7.6k
views
deseq2 correcting for batch effects
deseq2 batch effect removebatcheffect() design matrix
updated 8.1 years ago by 43k • written 8.1 years ago by ★ 1.5k
1
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2
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1.5k
views
DESeq2 design matrix with a single mock and multiple timepoints
deseq2 design matrix
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
0
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2
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3.8k
views
Time-course analysis with limma for >3 time points
limma contrast matrix design matrix multiple time points timecourse
updated 4.5 years ago by • 0 • written 8.4 years ago by ▴ 20
0
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0
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1.5k
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Possible confounding of variable of interest with batch covariate and Partial NA coefficients when including batch in limma linear model for microarr…
limma batch effect design matrix microarray confounding
8.5 years ago svlachavas ▴ 840
0
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7
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3.2k
views
DESeq2: how to identify confounding variable in the design matrix
deseq2 confounders design matrix rnaseq
8.6 years ago • updated 8.5 years ago lina.faller ▴ 10
3
votes
4
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6.2k
views
multiple comparison using limma
limma design matrix makecontrasts multiple comparisons
8.8 years ago annabelle.congras ▴ 10
7
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5
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2.1k
views
Which is the best design matrix to compare a timecourse between two conditions?
limma voom design matrix timecourse
updated 8.8 years ago by 53k • written 8.8 years ago by ▴ 10
2
votes
6
replies
4.6k
views
RNA-seq paired analysis design
paired samples design matrix limma deseq2 edger
updated 8.8 years ago by 53k • written 8.8 years ago by • 0
0
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8
replies
5.3k
views
Design question limma multi variables
limma design matrix
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 40
81 results • Page 1 of 2
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Replies
Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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