I'm using the function RUVg in the RUVSeq package to analyse my RNA-seq data. The output of RUVg consists of the factors of unwanted variation W and the normalised counts N. Could someone please tell me how the normalised counts N are calculated? See the formula below.
log E[Y |W, X, O] = W α + Xβ + O.
Are the normalised counts simply log(Y)-Wα-O? If so, how can I get α from the output of RUVg? Also, log(Y)-Wα-O wouldn't consist of integers, so why does the normalised counts matrix N produced by RUVg consist of counts?