Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

Background: Concerns are often raised about the accuracy of microarray technologies and the degree of cross-platform agreement, but there are yet no methods which can unambiguously evaluate precision and sensitivity for these technologies on a whole-array basis. Results: A methodology is described for evaluating the precision and sensitivity of whole-genome gene expression technologies such as microarrays. The method consists of an easy-to-construct titration series of RNA samples and an associated statistical analysis using non-linear regression. The method evaluates the precision and responsiveness of each microarray platform on a wholearray basis, i.e., using all the probes, without the need to match probes across platforms. An experiment is conducted to assess and compare four widely used microarray platforms. All four platforms are shown to have satisfactory precision but the commercial platforms are superior for resolving differential expression for genes at lower expression lev...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Andrew J. Holloway, Alicia Oshlack, Dileepa S. Diyagama, David D. L. Bowtell, Gordon K. Smyth
• Keywords: BMCBI 2006, Easy-to-construct Titration Series, Microarray Platforms, Whole-genome Gene Expression