LNNB-correlation-snippet.R
Code snipits and programs written in R, S or S-PLUS
- p (genes) by n (slides) matrix
- 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 <- (2.32501, sqrt(0.38106), sqrt(1.11561)) # "IPTG-a parameters" k <- 1000
mu <- params[1] sigma <- params[2] tau <- params[3]
kDE <- rgamma(2*m1, shape=k, rate=k) DEmeans <- rnorm(2*m1, mu, tau) DEmeans <- DEmeans * kDE
kEE <- rgamma(m0, shape=k, rate=k) EEmeans <- rnorm(m0 , mu, tau) EEmeans <- EEmeans * kEE
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)
- 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))
