Pre-processing Agilent microarray data

Background: Pre-processing methods for two-sample long oligonucleotide arrays, specifically the Agilent technology, have not been extensively studied. The goal of this study is to quantify some of the sources of error that affect measurement of expression using Agilent arrays and to compare Agilent's Feature Extraction software with pre-processing methods that have become the standard for normalization of cDNA arrays. These include log transformation followed by loess normalization with or without background subtraction and often a between array scale normalization procedure. The larger goal is to define best study design and pre-processing practices for Agilent arrays, and we offer some suggestions. Results: Simple loess normalization without background subtraction produced the lowest variability. However, without background subtraction, fold changes were biased towards zero, particularly at low intensities. ROC analysis of a spike-in experiment showed that differentially expres...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Marianna Zahurak, Giovanni Parmigiani, Wayne Yu, Robert B. Scharpf, David Berman, Edward Schaeffer, Shabana Shabbeer, Leslie Cope
• Keywords: Background Subtraction, BMCBI 2007, Loess Normalization, Simple Loess Normalization