Presence-Absence Calls on AffyMetrix HG-U133 Series Microarrays with panp

Introduction This document describes how to use panp to perform gene detection (make presence/absence calls) on AffyMetrix HG-U133 series microarray data. Currently, the HG-U133A and HG-U133 Plus 2.0 are supported. panp operates on preprocessed microarray expression data as an ExpressionSet object. Any preprocessing method can be used to create the ExpressionSet, such as rma(), mas5(), expresso(), or gcrma(). Examples show how to quickly create such an ExpressionSet, then how to use panp to generate a set of presence/absence calls and a set of p-values indicating significance of the detection for each expression value.