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Background  Various analytical methods exist that first quantify gene expression and then analyze differentially expressed genes from Affymetrix GeneChip ®  gene expression analysis array data. These methods differ in the choice of probe measure (quantification of probe hybridization), summarizing multiple probe intensities into a gene expression value, and analysis of differential gene expression. Research papers that describe these methods focus on performance, and how their approaches differ from others. To better understand the common features and differences between various methods, and to evaluate their impact on the results of gene expression analysis, we describe a class of models, referred to as generalized probe models (GPMs), which encompass various currently available methods.    Results  Using an empirical dataset, we compared different formulations of GPMs, and GPMs with three other commonly used methods, i.e. MAS 5.0, dChip, and RMA. The comparison shows that,   on a genome-wide scale   , different methods yield similar results if the same probe measures are chosen.    Conclusion  In this paper we present a general framework, i.e. GPMs, which encompasses various methods. GPMs permit the use of a wide range of probe measures and facilitate appropriate comparison between commonly used methods. We demonstrate that the dissimilar results stem primarily from different choice of probe measures, rather than other factors.

A class of models for analyzing GeneChip® gene expression analysis array data