PANP - a New Method of Gene Detection on Oligonucleotide Expression Arrays

Abstract. Currently, the method most used for gene detection calls on Affymetrix oligonucleotide arrays is provided as part of the MAS5.0 software. The MAS method uses Wilcoxon statistics for determining presence-absence (MASP/A) calls. It is known that MAS-P/A is limited by its need to use both perfect match (PM) and mismatch (MM) probe data in order to call a gene present or absent. A considerable amount of recent research has convincingly shown that using MM data in gene expression analysis is problematic. The RMA method, which uses PM data only, is one method that has been developed in response to this. However, there is no publicly available method outside of MAS-P/A to establish presence or absence of genes from microarray data. It seems desirable to decouple the method used to generate gene expression values from the method used to make gene detection calls. We have therefore developed a statistical method in R, called Presence-Absence calls with Negative Probesets (PANP) which ...

• Type: Conference
• Year: 2007
• Where: BIBE
• Authors: Peter Warren, Deanne Taylor, Paolo G. V. Martini, Jennifer Jackson, Jadwiga R. Bienkowska
• Keywords: BIBE 2007, Bioinformatics, Gene Detection Calls, Gene Expression, Method Uses Wilcoxon