Data distribution of short oligonucleotide expression arrays and its application to the construction of a generalized intellectual framework.

Information obtained by microarray studies frequently cause discrepancies between projects, laboratories and/or even repeated experiments. Such inconsistencies may be due to the lack of generality in the intellectual frameworks that form the basis for understanding the data. This article proposes a parametric framework that can handle a wide range of experimental data obtained by GeneChip expression arrays. The framework is based on a parsimonious model, which has been developed according to thermodynamic estimations of the process of hybridization. Using the model, probe data were normalized and summarized into gene expression levels. Verification of the appropriateness of the model is demonstrated statistically by the use of real data obtained from several project series. Furthermore, improved stabilities in changes in expression are observed in comparison with other currently used methods. Estimations of transcriptome differences between organs coincided between various projects.