Preprocessing Illumina Whole Genome Expression BeadChips

This R package provides:

  1. strip-level normalization and plotting;
  2. "normexp" background correction aided by negative controls.

Package Downloads


For strip-level normalization, please cite:

Shi, W, Banerjee, A, Ritchie, ME, Gerondakis, S, and Smyth, GK (2009). Illumina WG-6 BeadChip strips should be normalized separately. BMC Bioinformatics 10, 372. [Full Text]


This package is recommended only for version 1 of Illumina WG-6 BeadChips. For later types of Illumina arrays, please use the limma package instead.