Calculation of normalised counts about mdseq

[zjdaye]

Hi Aedan,

Thanks for your comment! We used the simple convention of normalizing with normalized count = raw count / normalization factor that had been used by earlier authors. I had discussed your comment with my co-author Di Ran. His view is that one might correct the normalization factor with library size by
ef <- lib.size * norm.factors # effective library size that is on the scale of count
nf.final <- ef/ exp(mean(log(ef))) # normalize around 1
and replace norm.factors with nf.final for normalization.

Hope this is helpful!

Best,
John.