Assessing Statistical Significance in Microarray Experiments Using the Distance Between Microarrays

We propose a method to compare the location and variability of gene ex-pression between two groups of microarrays using a permutation test based on the pairwise distance between microarrays. The microarrays could be samples from distinct clinical or biological populations or microarrays prepared at two different levels of an experimental factor. For these tests the entire microarray or some pre-specifed subset of genes, not the individual gene, is the unit of analysis. We apply this method to compare results from two dfferent protocols for preparing labeled targets for microarray hybridization and their subsequent gene expression analysis. Keywords: Comparative genomic expression Overall design - Splenocytes were extracted from six sham mice and six trauma-hemorrhagic mice. Total RNA was prepared from individual mice and labeled as targets by two different methods for analysis on Affymentrix MOE 430 2+chips.