Comparison of Normalizing Procedures for Oligonucleotide Arrays

• Activity Number: 346
• Type: Topic Contributed
• Date/Time: Wednesday, August 14, 2002 : 2:00 PM to 3:50 PM
• Sponsor: Biopharmaceutical Section*
• Author(s): Magnus Astrand*+
• Affiliation(s): AstraZeneva R&D Molndal
• Keywords: gene expression ; oligonucleotide array ; normalization

Abstract

Affymetrix high-density oligonucleotide arrays constitute a tool that has the capacity to simultaneously measure the abundance of thousands of mRNA sequences in biological samples.

In order to allow direct array-to-array comparisons, normalization is a necessity. When deciding on an appropriate normalization procedure, there are a couple of questions that need to be addressed, e.g., on which level should the normalization be performed: on the level of feature intensities or on the level of expression indices? Should all features/expression indices be used, or can we choose a subset of features likely to be un-regulated?

Another question is how to actually perform the normalization: normalize using the overall mean intensity or use a smooth normalization curve? Most of the currently used normalization methods are linear, e.g., the normalization method implemented in the Affymetrix software GeneChip is based on the overall mean intensity. However, along with alternative methods of summarizing feature intensities into an expression index, nonlinear methods have recently started to appear. A couple of such methods will be discussed and compared.