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. In aCGH data, systematic errors are comparable to those occurring in transcriptome data. However, especially for microbes, an additional source of variation exists: differences in hybridization due to gene sequence divergence between the strains hybridized. Current normalization methods do not take this source of variation into consideration. Results We present Supervised Lowess, or S-Lowess, an application of the subset Lowess normalization method that does take difference in genomic content into account. The performance of S-Lowess was assessed on aCGH experiments in which differentially labeled genomic DNA fragments of Lactococcus lactis IL1403 and L. la

ORGANISM(S): Lactococcus lactis subsp. cremoris MG1363

SUBMITTER: Sacha van Hijum 

PROVIDER: E-GEOD-9039 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress