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Model matrix for longitudinal pairwise rna-seq data: linear regression or linear mixed model?
limma model matrix linear regression
5.7 years ago agm • 0
1
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2
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1.7k
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DESeq2 design & model matrix not full rank - am I nesting correctly?
deseq2 model matrix experimental design multiple factor design
updated 7.2 years ago by 43k • written 7.2 years ago by • 0
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7
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1.7k
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Model matrix not full rank
deseq2 linear combination model matrix
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
2
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4
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1.5k
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Removing batch effect on edgeR when interactons are looked at
rnaseq edger statistics model matrix
updated 7.5 years ago by ★ 13k • written 7.5 years ago by ▴ 90
3
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6
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30k
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Designing a contrast in DESEQ
deseq2 design and contrast matrix model matrix
8.1 years ago mrigaya.mehra ▴ 10
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2.1k
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DESeq2 glibc error
deseq2 differential gene expression model matrix
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
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6
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2.9k
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Find if a covariate has effect on gene expression level using edgeR and DESeq2
edger deseq2 model matrix differential expression
8.5 years ago ta65 • 0
2
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7
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3.5k
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ballgown custom models
ballgown linear model model matrix custom model
9.0 years ago • updated 8.9 years ago sbcn ▴ 80
7
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6
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4.4k
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Design and contrast question limma (additive or nested or duplicateCorrelation())??
limma model matrix limma design matrix complex-design
updated 9.8 years ago by ★ 28k • written 9.8 years ago by ★ 4.1k
9
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Limma Model Matrix Understanding
limma limma design matrix model matrix
updated 9.9 years ago by ★ 28k • written 9.9 years ago by ▴ 370
2
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5
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4.4k
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design model matrix for nested factors (edgeR)
edger design matrix model matrix
updated 9.9 years ago by ★ 28k • written 9.9 years ago by • 0
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Comment: DESEQ2 looking at main effects while controlling for a continuous variable by James W. MacDonald 68k
The covariate is accounted for when you fit the model, so you don't need to do anything with it at the contrast step. You don't need a con…
Comment: DESEQ2 looking at main effects while controlling for a continuous variable by Lennie • 0
Thank you so much for taking the time and for the detailed explanation! I was wondering, in your numeric contrast of c(1, -1, 0,0,0), doe…
Answer: DESEQ2 looking at main effects while controlling for a continuous variable by James W. MacDonald 68k
If you use a factor effects model (with an intercept), then you will have a baseline group (the intercept), and all other coefficients exce…
Comment: Issue with DECIPHER::IdTaxa by Daniel • 0
The issue is still there and it is a real pain. ape and ade4 are used by packages like Phyloseq. There should be a way to avoid these inc…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Gordon Smyth 52k
I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…
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Answer: DESEQ2 looking at main effects while controlling for a continuous variable
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
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