updated 3.0 years ago by
thomas.nigel.lawson
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written 3.3 years ago by
hp71727
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Answer: Array weights in dpcDE
by
Gordon Smyth
53k
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
43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice
by
Gordon Smyth
53k
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…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2
by
chp265
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0
Good point, I hadn't considered the fact quantitative `time` implies a (logit-)linear response *to* time. You're correct that I haven't exp…
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