Cross-hybridization modeling on Affymetrix exon arrays.

ABSTRACT:

Motivation

Microarray designs have become increasingly probe-rich, enabling targeting of specific features, such as individual exons or single nucleotide polymorphisms. These arrays have the potential to achieve quantitative high-throughput estimates of transcript abundances, but currently these estimates are affected by biases due to cross-hybridization, in which probes hybridize to off-target transcripts.

Results

To study cross-hybridization, we map Affymetrix exon array probes to a set of annotated mRNA transcripts, allowing a small number of mismatches or insertion/deletions between the two sequences. Based on a systematic study of the degree to which probes with a given match type to a transcript are affected by cross-hybridization, we developed a strategy to correct fo

SUBMITTER: Kapur K 

PROVIDER: S-EPMC2639301 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature