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Creating a design matrix
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80
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1
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Design Matrix with paired and independent samples plus RUVg Spike-in normalization
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Design matrix for a two-color experimental design testing for time effect on 3 treated cell-lines, each with its own time=0 control
microarray twochannel limma design matrix written 6 weeks ago by rubi • 90 • updated 6 weeks ago by Gordon Smyth ♦ 35k
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128
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Design matrix for regressing gene expression on a continuous variable - age
limma R lmfit design matrix written 8 weeks ago by anupriya.dalmia • 0 • updated 8 weeks ago by Aaron Lun • 21k
2
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117
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1
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Am I on the right tracks with a 3 factor design in Limma?
biobase limma R design matrix written 11 weeks ago by reubenmcgregor88 • 0 • updated 11 weeks ago by Gordon Smyth ♦ 35k
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266
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Test for differential variability with missMethyl (DiffVar) using block design
limma block design matrix missmethyl diffvar written 15 months ago by Simone • 170 • updated 3 months ago by lhuang7 • 10
4
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155
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edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression design matrix model.matrix written 4 months ago by grabear • 0 • updated 4 months ago by Gordon Smyth ♦ 35k
3
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2
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124
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single continuous factor
edger design matrix continuous written 4 months ago by ashley.lu • 0 • updated 4 months ago by Gordon Smyth ♦ 35k
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2
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121
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Limma design matrix
limma design matrix written 4 months ago by R • 40 • updated 4 months ago by Gordon Smyth ♦ 35k
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152
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1
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RNAseq DESeq2 paired data design help
rnaseq deseq2 design matrix written 5 months ago by umlch • 0 • updated 4 months ago by Michael Love ♦ 19k
1
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1
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142
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1
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DESEQ2 design with multiple conditions
deseq2 design matrix written 4 months ago by vrehaman • 0 • updated 4 months ago by Michael Love ♦ 19k
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1
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164
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1
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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 written 5 months ago by khhsource • 0 • updated 5 months ago by Michael Love ♦ 19k
3
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179
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EdgeR model formula design matrix
edger design matrix paired samples written 5 months ago by aiko • 0 • updated 5 months ago by Aaron Lun • 21k
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146
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differential expression analysis of cell subtypes mixture
edger deseq2 design matrix multifactorial design written 6 months ago by Assa Yeroslaviz • 1.4k • updated 6 months ago by Aaron Lun • 21k
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178
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1
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edgeR design matrix
edger design and contrast matrix design matrix written 6 months ago by cafelumiere12 • 20 • updated 6 months ago by Gordon Smyth ♦ 35k
1
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1
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159
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1
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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 written 6 months ago by jaime.alvarez.benayas • 0
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409
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LIMMA : group specific effect of a treatment while controlling for individual effect
limma limma design matrix design matrix limma-voom limma time-course written 6 months ago by SPbeginner • 0
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2
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335
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Microarray expression analysis for on factor taking account confounders (covariables)
limma design matrix matrix with covariables written 7 months ago by michel655 • 0 • updated 6 months ago by Aaron Lun • 21k
3
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1
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443
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1
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DESeq2 batch effect with and without interaction model
deseq2 R linear model rna-seq design matrix written 10 months ago by gdagstn • 0 • updated 10 months ago by Michael Love ♦ 19k
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2
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585
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2
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stimulation effects between wild-type and knockout cells using deseq
deseq2 interactions multiple factor design design matrix written 2.8 years ago by Assa Yeroslaviz • 1.4k • updated 10 months ago by Michael Love ♦ 19k
2
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268
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1
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complex design for chip-seq analysis
chipseq limma multiple factor design design matrix csaw written 11 months ago by Assa Yeroslaviz • 1.4k • updated 11 months ago by Aaron Lun • 21k
1
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1
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932
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1
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deseq2 correcting for batch effects
deseq2 removebatcheffect() batch effect design matrix written 11 months ago by Assa Yeroslaviz • 1.4k • updated 11 months ago by Michael Love ♦ 19k
1
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1
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451
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1
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DESeq2 design matrix with a single mock and multiple timepoints
deseq2 design matrix written 13 months ago by ap3637 • 0 • updated 13 months ago by Michael Love ♦ 19k
0
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1
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269
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1
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Time-course analysis with limma for >3 time points
timecourse limma design matrix multiple time points contrast matrix written 14 months ago by relathman • 0 • updated 14 months ago by James W. MacDonald ♦ 47k
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357
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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 microarray data
microarray limma batch effect design matrix confounding written 16 months ago by svlachavas • 610
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