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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
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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?
Answer: voomLmFit fitted log-CPM values
by
Gordon Smyth
53k
Fitted values are obtained from limma MArrayLM objects by
```
fitted(v)
```
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