Supervised Lowess normalization of comparative genome hybridization data--application to lactococcal strain comparisons.

ABSTRACT:

Background

Array-based comparative genome hybridization (aCGH) is commonly used to determine the genomic content of bacterial strains. Since prokaryotes in general have less conserved genome sequences than eukaryotes, sequence divergences between the genes in the genomes used for an aCGH experiment obstruct determination of genome variations (e.g. deletions). Current normalization methods do not take into consideration sequence divergence between target and microarray features and therefore cannot distinguish a difference in signal due to systematic errors in the data or due to sequence divergence.

Results

We present supervised Lowess, or S-Lowess, an application of the subset Lowess normalization method. By using a predicted subset of array features with minimal sequence di

SUBMITTER: van Hijum SA 

PROVIDER: S-EPMC2275246 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature