Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays.

ABSTRACT:

Background

High-density oligonucleotide arrays (HDONAs) are a powerful tool for assessing differential mRNA expression levels. To establish the statistical significance of an observed change in expression, one must take into account the noise introduced by the enzymatic and hybridization steps, called type I noise. We undertake an empirical characterization of the experimental repeatability of results by carrying out statistical analysis of a large number of duplicate HDONA experiments.

Results

We assign scoring functions for expression ratios and associated quality measures. Both the perfect-match (PM) probes and the differentials between PM and single-mismatch (MM) probes are considered as raw intensities. We then calculate the log-ratio of the noise structure using robust

SUBMITTER: Naef F 

PROVIDER: S-EPMC115253 | biostudies-literature | 2002

REPOSITORIES: biostudies-literature