Good day,
Now I notice the differences in how the prior counts are applied. In edgeR's
cpm:
prior.count.scaled <- lib.size/mean(lib.size) * prior.count
lib.size <- lib.size + 2 * prior.count.scaled
... ...
t(x) + prior.count.scaled
but in limma's voom:
t(counts + 0.5)/(lib.size + 1)
Basically, the values added to the counts and the library size ignore the
library size of each sample in the voom function.
--------------------------------------
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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