Bioconductor Modelmatrix

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limma modelmatrix

updated just now by Gordon Smyth 51k • written 1 day ago by kyj2226 • 0

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ALDEx2 modelmatrix covariates

16 months ago amir • 0

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4

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DESeq2 limma modelmatrix edgeR designmatrix

updated 3.1 years ago by Gordon Smyth 51k • written 3.1 years ago by rebecca.lea.johnston • 0

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5

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interactionterm edgeR modelmatrix

3.8 years ago ahsindoomilup • 0

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Answer: [How to construct a model.matrix ] by Gordon Smyth 51k

> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…

Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0

Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…

Comment: Merge Replicates vs Mixed Model by abadgerw • 0

@gabrielhoffman any insight?

Comment: makeContrastsDream for Interaction by abadgerw • 0

@gabrielhoffman any insight?

Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta by Michael Love 42k

That is the rows that did converge.

Votes

A: Some questions for remove batch effect by using mnnCorrect

A: Recommendations for combining multiple 10x runs into one SingleCellExperiment

Answer: [How to construct a model.matrix ]

Answer: Handling biological replicates in DESeq2

Comment: biomaRt rnorvegicus_gene_ensembl not available anymore

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