Bioconductor RMS

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RMS RPKM MEDIPS

updated 7.5 years ago by Lukas Chavez ▴ 570 • written 7.6 years ago by enrique.yeh ▴ 10

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Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by yongjie.wang • 0

Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…

Comment: European Bioconductor Conference 2023 planning by magnificent.mollusk.nvtp • 0

I once co-organized a genomics meetup where logistics, speaker balance, and outreach felt like solving a live [connections game](https://co…

Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k

I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …

Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k

> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…

Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k

The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…

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A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

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