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