**0**wrote:

In EdgeR, the 'log cpm' values are calculated as:

log2(t( (t(x)+prior.count.scaled) / lib.size ))

However, before that the library size is offset as:

lib.size <- lib.size+2*prior.count.scaled

I do not understand the factor of '2'. We add the prior to all counts, so I could understand it if we adjusted the library size by adding the number of genes times the prior, e.g.:

lib.size <- lib.size+(numberOfGenes)*prior.count.scaled

I noticed that voom does something similar:

t(log2(t(counts + 0.5)/(lib.size + 1) * 1e+06))

where we again have a library offset of '1', which is twice the prior.

Can anyone help me out here?

Best, Mikael Christensen