inst/samples/test06-sam.R

In ClassComparison: Classes and Methods for "Class Comparison" Problems on Microarrays

ng <- 10000
ns <- 50
nd <- 100
dat <- matrix(rnorm(ng*ns), ncol=ns)
dat[1:nd, 1:(ns/2)] <- dat[1:nd, 1:(ns/2)] + 2
dat[(nd+1):(2*nd), 1:(ns/2)] <- dat[(nd+1):(2*nd), 1:(ns/2)] - 2
cla <- factor(rep(c('A', 'B'), each=25))

res <- Sam(dat, cla)
plot(res)

plot(res, tracks=1:3)

summary(res)
summary(res, cutoff=2)

a <- summary(res)
plot(a@significant.calls)
plot(a@significant.calls[1:300])

countSignificant(res, 1)

rm(ng, ns, nd, dat, cla, res, a)