Difference between revisions of "LNNB-snippet.R"
From Organic Design wiki
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# p (genes) by n (slides) matrix | # p (genes) by n (slides) matrix | ||
# m=p keeping fdr notation | # m=p keeping fdr notation | ||
Latest revision as of 00:39, 6 June 2007
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]
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)
- 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))
