Bioconductor Mixedmodel

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variancePartition mixedmodel dream

2.0 years ago hayleyw • 0

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mixedmodel

4.3 years ago veronique.storme • 0

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variancepartition lme4 mixedmodel

updated 5.9 years ago by gabriel.hoffman ▴ 170 • written 6.0 years ago by c.taylor • 0

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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…

Comment: voomLmFit fitted log-CPM values by Lina ▴ 10

Is the output from fitted(v) in the log2 CPM scale? or CPM scale?

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A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

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