Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by c

Background: Gene expression profiling using microarrays has become an important genetic tool. Spotted arrays prepared in academic labs have the advantage of low cost and high design and content flexibility, but are often limited by their susceptibility to quality control (QC) issues. Previously, we have reported a novel 3-color microarray technology that enabled array fabrication QC. In this report we further investigated its advantage in spot-level data QC. Results: We found that inadequate amount of bound probes available for hybridization led to significant, gene-specific compression in ratio measurements, increased data variability, and printing pin dependent heterogeneities. The impact of such problems can be captured through the definition of quality scores, and efficiently controlled through quality-dependent filtering and normalization. We compared gene expression measurements derived using our data processing pipeline with the known input ratios of spiked in control clones, a...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Xujing Wang, Shuang Jia, Lisa Meyer, Bixia Xiang, Li-Yen Chen, Nan Jiang, Carol Moreno, Howard J. Jacob, Soumitra Ghosh, Martin J. Hessner
• Keywords: BMCBI 2006, Fabrication Qc, Gene Expression, Important Genetic Tool