wiki:SOPs/normalizePublic

Normalizing From the Same Platform

If the arrays of interest are of the same platform, follow the same procedure as outlined in normalizing microarrays.

Normalizing From Different Platforms

If the samples for normalizing are from different platforms,

Quantile

  1. Normalize arrays that belong to the same platform together
  2. Once normalized platform-specific, quantile normalize to produce the same distribution across all arrays.

  library(limma)
  # Read the data
  data = read.delim(myFile)
  # Quantile normalize 
  data.quantile_normalize = normalizeQuantiles(data[,c(2:ncol(data))])

Other