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Recent ...
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Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
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I'm not familiar with this usage, or code here
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normFactors <- exp(-1 * offst(set2))
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> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0
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The fitted values are on the log2CPM scale. I would have told you if they were not!
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Is the output from fitted(v) in the log2 CPM scale? or CPM scale?
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Fitted values are obtained from limma MArrayLM objects by
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fitted(v)
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