Bioconductor Glmlrt

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edger design matrix glmlrt

updated 7.9 years ago by Aaron Lun ★ 28k • written 7.9 years ago by simarsidhu25 • 0

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rna-seq edger glmlrt interactions

updated 8.7 years ago by Gordon Smyth 52k • written 8.7 years ago by David R ▴ 90

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6

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EdgeR data.frame glmLRT

updated 9.3 years ago by Gordon Smyth 52k • written 9.3 years ago by amoltej ▴ 10

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Comment: Crossover design with limma by SamGG ▴ 360

IMHO, here are the missing annotations treatmentdrug_orderDrugPlac - treatmentplacebo_orderDrugPlac, # effect of drug for the Drug…

Answer: What type of counts data to import for performing Isoform analysis in edgeR by ATpoint ★ 4.5k

You don't need any of these files. You need the `catchSalmon` function which reads `quant.sf` and the inferential (Bootstrap/Gibbs) replica…

Comment: makeContrastsDream for Interaction by abadgerw • 0

Thank you! I will try this out.

Comment: Merge Replicates vs Mixed Model by abadgerw • 0

Thanks, @gabrielhoffman The data is actually proteomics so it is intensity data which is why I did not use voom but rather ran ebayes wi…

Comment: ANOVA like approach of edgeR by Gordon Smyth 52k

To identify common upregulated or downregulated genes, you would need to test for media condition contrasts for each cell type separately, …

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Comment: Crossover design with limma

Answer: DESeq2 normalization vs VST vs rlog

Comment: makeContrastsDream for Interaction

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