Evaluation of methods for oligonucleotide array data via quantitative real-time PCR

Background: There are currently many different methods for processing and summarizing probelevel data from Affymetrix oligonucleotide arrays. It is of great interest to validate these methods and identify those that are most effective. There is no single best way to do this validation, and a variety of approaches is needed. Moreover, gene expression data are collected to answer a variety of scientific questions, and the same method may not be best for all questions. Only a handful of validation studies have been done so far, most of which rely on spike-in datasets and focus on the question of detecting differential expression. Here we seek methods that excel at estimating relative expression. We evaluate methods by identifying those that give the strongest linear association between expression measurements by array and the "gold-standard" assay. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) is generally considered the "gold-standard" assay ...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Li-Xuan Qin, Richard P. Beyer, Francesca N. Hudson, Nancy J. Linford, Daryl E. Morris, Kathleen F. Kerr
• Keywords: Background Adjustment, BMCBI 2006, Mismatch Probes, Scientific Question