LNNB-snippet.R

1. p (genes) by n (slides) matrix
2. m=p keeping fdr notation

m <- p <- 1000 nreps <- 5

n <- nreps * 2 pi0 <- 0.95

m1 <- round(m * (1-pi0)) m0 <- p - m1

params <- c(2.74886, 1.36546, 4.12844) # "IPTG-a parameters" k <- 1000

mu <- params[1] sigma <- params[2] tau <- params[3]

DEmeans <- rnorm(2*m1, mu, tau) EEmeans <- rnorm(m0 , mu, tau) means <- c(rep(DEmeans, each=nreps),rep(EEmeans, each=2*nreps)) X <- exp(rnorm(n*p, means, sigma)) dim(X) <- c(n,p) X <- t(X)

1. Graphical check

hist(kDE, prob=TRUE) lines(density(kDE))

hist(kEE, prob=TRUE) lines(density(kEE))

Xbar <- rowMeans(log2(X)) hist(Xbar, breaks=30, prob=TRUE) lines(density(Xbar)) pairs(log2(X))