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Comment: 3-factor DESeq2 trime-series analysis
by
swbarnes2
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What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…
Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
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yongjie.wang
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Thanks for your reply.
" normFactors <- exp(-1 * offst(set2))
normFactors <- normFactors / exp(rowMeans(log(normFactors)))
normalizat…
Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
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Michael Love
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I'm not familiar with this usage, or code here
```
normFactors <- exp(-1 * offst(set2))
```
In the RNA-seq gene-level workflow, we …
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> 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
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Gordon Smyth
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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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