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James W. MacDonald
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written 10 months ago by
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updated 4.5 years ago by
James W. MacDonald
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written 4.5 years ago by
diego.bardiaux
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updated 4.7 years ago by
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written 4.8 years ago by
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written 8.6 years ago by
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Answer: lfc shrinkage estimator in DESeq2
by
plumsgorillas
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You are on the right track. In DESeq2, raw log2 fold changes are often noisy and can be misleading, especially for genes with low counts. A…
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The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights.
However,…
Answer: lfc shrinkage estimator in DESeq2
by
Michael Love
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Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice
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Gordon Smyth
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The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice
by
SamGG
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360
Thanks for your feedback and for reassuring me. :-)
As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
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