tests/normalizeQuantileRank.list.R

In HenrikBengtsson/aroma.light-BioC_release: Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

library("aroma.light")

# Simulate ten samples of different lengths
N <- 10000
X <- list()
for (kk in 1:8) {
  rfcn <- list(rnorm, rgamma)[[sample(2, size=1)]]
  size <- runif(1, min=0.3, max=1)
  a <- rgamma(1, shape=20, rate=10)
  b <- rgamma(1, shape=10, rate=10)
  values <- rfcn(size*N, a, b)

  # "Censor" values
  values[values < 0 | values > 8] <- NA

  X[[kk]] <- values
}

# Add 20% missing values
X <- lapply(X, FUN=function(x) {
  x[sample(length(x), size=0.20*length(x))] <- NA;
  x
})

# Normalize quantiles
Xn <- normalizeQuantile(X)

# Plot the data
layout(matrix(1:2, ncol=1))
xlim <- range(X, na.rm=TRUE);
plotDensity(X, lwd=2, xlim=xlim, main="The original distributions")
plotDensity(Xn, lwd=2, xlim=xlim, main="The normalized distributions")