As I want to understand why a scoring line on the so-called SAM plot could be not parallel to the diagonal I go back to the doc. There is a similar example, example C p 21.
I tried to reproduce it using the given formula (p 19-20), but I don't a similar plot.
I will appreciate any help to understand such a plot or to correct the simulation formula.
library(samr) set.seed(0) nr = 1000 ns = 4 edat = matrix(rnorm(nr*ns*2), nrow = nr) exC = edat + matrix(c(rep(0, nr*ns), rnorm(nr*ns, mean = 0, sd = 8)), nrow = nr) heatmap(exC, Rowv = NA, Colv = NA) exC.sam = samr(list(x = exC[,c(1:3,5,4,6:8)], y = c(rep(1, ns), rep(2, ns)), logged2 = TRUE), resp.type = "Two class unpaired", assay.type = "array") samr.plot(exC.sam, 0.5)