[Bioc-devel] edgeR and limma Default Offsets

[Dario Strbenac]

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.

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Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia