Bioconductor Downregulated genes

Showing : downregulated genes • reset

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typo NES rwikipathways downregulated genes gene set enrichment analysis

updated 5.7 years ago by alex.pico ▴ 30 • written 6.0 years ago by Fischer-philipp ▴ 30

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edger differential gene expression upregulated genes downregulated genes

updated 6.6 years ago by lisacarlon25 • 0 • written 6.6 years ago by fawazfebin ▴ 60

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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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