Quintile normalization

gistfile1.r

# Create a refernce distribution using the median of all samples
ref <- apply(apply(data.normalized[,3:ncol(data.normalized)],
                   2,
                   FUN=sort),
             1,
             FUN=median)
# Create a emperical cdf function for the reference distribution
ref.cdf <- ecdf(ref)

# Quintile normalize!
data.qn <- apply(data.normalized[,3:ncol(data.normalized)], 2, function(d) {
  sample.cdf <- ecdf(d)
  return(quantile(ref.cdf, sample.cdf(d))) })