Bioconductor Model matrix

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limma model matrix linear regression

5.6 years ago • updated 5.5 years ago agm • 0

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deseq2 model matrix experimental design multiple factor design

updated 7.0 years ago by Michael Love 43k • written 7.0 years ago by amye107 • 0

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deseq2 linear combination model matrix

updated 7.3 years ago by Michael Love 43k • written 7.3 years ago by sally_b86 • 0

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rnaseq edger statistics model matrix

updated 7.3 years ago by Steve Lianoglou ★ 13k • written 7.3 years ago by David R ▴ 90

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deseq2 design and contrast matrix model matrix

7.9 years ago mrigaya.mehra ▴ 10

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deseq2 differential gene expression model matrix

updated 8.0 years ago by Michael Love 43k • written 8.0 years ago by gregory.l.stone ▴ 10

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edger deseq2 model matrix differential expression

8.4 years ago ta65 • 0

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ballgown linear model model matrix custom model

8.9 years ago • updated 8.8 years ago sbcn ▴ 80

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limma model matrix limma design matrix complex-design

updated 9.6 years ago by Aaron Lun ★ 28k • written 9.6 years ago by Guido Hooiveld ★ 4.1k

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limma limma design matrix model matrix

updated 9.7 years ago by Aaron Lun ★ 28k • written 9.7 years ago by andrew.j.skelton73 ▴ 370

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edger design matrix model matrix

updated 9.8 years ago by Aaron Lun ★ 28k • written 9.8 years ago by silvia.paolucci81 • 0

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Comment: contrast matrix design for a continuous variable by dtzhu337 • 0

Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…

Answer: SingleCellExperiment convenience function for metadata+expression? by Peter Hickey ▴ 740

Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…

Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10

Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…

Comment: EdgeR Biological CVs by ATpoint ★ 4.6k

"Joseph" is a spam bot...

Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k

GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…

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How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.

Answer: EdgeR Biological CVs

Answer: Error in download.file for TCGAutils::symbolsToRanges

Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?

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