(1) Biometric Research Branch, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA;(2) The EMMES Corporation, Rockville, Maryland, USA
Abstract:
Background
Normalization is a critical step in analysis of gene expression profiles. For dual-labeled arrays, global normalization assumes
that the majority of the genes on the array are non-differentially expressed between the two channels and that the number
of over-expressed genes approximately equals the number of under-expressed genes. These assumptions can be inappropriate for
custom arrays or arrays in which the reference RNA is very different from the experimental samples.