Extended analysis of benchmark datasets for Agilent two-color microarrays

Background: As part of its broad and ambitious mission, the MicroArray Quality Control (MAQC) project reported the results of experiments using External RNA Controls (ERCs) on five microarray platforms. For most platforms, several different methods of data processing were considered. However, there was no similar consideration of different methods for processing the data from the Agilent two-color platform. While this omission is understandable given the scale of the project, it can create the false impression that there is consensus about the best way to process Agilent two-color data. It is also important to consider whether ERCs are representative of all the probes on a microarray. Results: A comparison of different methods of processing Agilent two-color data shows substantial differences among methods for low-intensity genes. The sensitivity and specificity for detecting differentially expressed genes varies substantially for different methods. Analysis also reveals that the ERCs...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Kathleen F. Kerr
• Keywords: Agilent Two-color Data, Agilent Two-color Platform, BMCBI 2007, ERCs