Hi, I have some doubts on cpm function in edgeR package. Given this initial part of the code:

> library(edgeR)
> data_clean<- read.table("unito.txt", header = TRUE)
> 
> group<-factor(c("A", "A", B","B"))
> 
> y <- DGEList(counts=data_clean,group=group)
> 
> y <- calcNormFactors(y)

I obtain different values if I calculate cpm in this way

> cpm <- cpm(y, log = FALSE, normalized.lib.sizes=TRUE)

Or in this one

> cpm <- cpm(y$counts, log = FALSE, normalized.lib.sizes=TRUE)

Why are them different? What does it change? What is the correct way to calculate them? I noticed that if I calculate them with the standard formula "by hand", I obtain the same values as the second formula (y$counts). In the edge manual it seems just to use the y argument.

Thank you, Francesca