Efficiency clustering for low-density microarrays and its application to QPCR

Background: Pathway-targeted or low-density arrays are used more and more frequently in biomedical research, particularly those arrays that are based on quantitative real-time PCR. Typical QPCR arrays contain 96-1024 primer pairs or probes, and they bring with it the promise of being able to reliably measure differences in target levels without the need to establish absolute standard curves for each and every target. To achieve reliable quantification all primer pairs or array probes must perform with the same efficiency. Results : Our results indicate that QPCR primer-pairs differ significantly both in reliability and efficiency. They can only be used in an array format if the raw data (so called CT values for real-time QPCR) are transformed to take these differences into account. We developed a novel method to obtain efficiency-adjusted CT values. We introduce transformed confidence intervals as a novel measure to identify unreliable primers. We introduce a robust clustering algorit...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Eric F. Lock, Ryan Ziemiecki, J. S. Marron, Dirk P. Dittmer
• Keywords: BMCBI 2010, Confidence Intervals, Primer Pair, Quantitative Real-time Pcr