Difference between revisions of "GGBsnippet.R"
From Organic Design wiki
(Make script functional and use IPTG-a parameters) |
(Make script functional and use IPTG-a parameters) |
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| Line 27: | Line 27: | ||
X <- t(X) | X <- t(X) | ||
| + | # Graphical check | ||
pairs(log2(X)) | pairs(log2(X)) | ||
Revision as of 23:36, 28 August 2006
- p (genes) by n (slides) matrix
- m=p keeping fdr notation
p <- m <- 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"
a.shape <- params[1] a0.shape <- params[2] scale <- params[3]
DEscales <- rgamma(2*m1, shape=a0.shape, rate=scale) EEscales <- rgamma(m0 , shape=a0.shape, rate=scale)
scales <- c(rep(DEscales, each=nreps), rep(EEscales, each=2*nreps)) # same as p
X <- rgamma(n* p, a.shape, rate=scales) dim(X) <- c(n,p)
X <- t(X)
- Graphical check
pairs(log2(X))
