(1) Laboratory for High Performance Computing and Informatics and Section of Molecular and Cellular Biology University of California Davis MCB, One Shields Avenue Davis, CA 95616, USA
Abstract:
Background
Life processes are determined by the organism's genetic profile and multiple environmental variables. However the interaction
between these factors is inherently non-linear 1]. Microarray data is one representation of the nonlinear interactions among genes and genes and environmental factors. Still
most microarray studies use linear methods for the interpretation of nonlinear data. In this study, we apply Isomap, a nonlinear
method of dimensionality reduction, to analyze three independent large Affymetrix high-density oligonucleotide microarray
data sets.