Novel definition files for human GeneChips based on GeneAnnot

Background: Improvements in genome sequence annotation revealed discrepancies in the original probeset/gene assignment in Affymetrix microarray and the existence of differences between annotations and effective alignments of probes and transcription products. In the current generation of Affymetrix human GeneChips, most probesets include probes matching transcripts from more than one gene and probes which do not match any transcribed sequence. Results: We developed a novel set of custom Chip Definition Files (CDF) and the corresponding Bioconductor libraries for Affymetrix human GeneChips, based on the information contained in the GeneAnnot database. GeneAnnot-based CDFs are composed of unique custom-probesets, including only probes matching a single gene. Conclusion: GeneAnnot-based custom CDFs solve the problem of a reliable reconstruction of expression levels and eliminate the existence of more than one probeset per gene, which often leads to discordant expression signals for the s...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, Alexandra Sirota, Marilyn Safran, Michael Shmoish, Sergio Ferrari, Doron Lancet, Gian Antonio Danieli, Silvio Bicciato
• Keywords: Affymetrix, Affymetrix Human Genechips, BMCBI 2007, Gene