Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays.

ABSTRACT:

Background

Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls in the original Affymetrix probe annotation have been described; however, few studies have provided rigorous solutions for routine data analysis.

Results

Using AceView, a comprehensive human transcript database, we have reannotated the probes by matching them to RNA transcripts instead of genes. Based on this transcript-level annotation, a new probe set definition was created in which every probe in a probe set maps to a common set of AceView gene transcripts. In addition, using artificial data sets we identified that a minimal probe set size of 4 is necessary for reliable statistical summarization.

SUBMITTER: Lu J 

PROVIDER: S-EPMC1853115 | biostudies-literature | 2007 Mar

REPOSITORIES: biostudies-literature