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Quality control (QC) is crucial for any scientific method producing Applying adequate QC introduces new challenges in the genomics field amounts of data are produced with complex technologies. For DNA specific algorithms for QC and pre-processing including normalization developed by the scientific community, especially for expression chips Affymetrix platform. Many of these have been implemented in the scripting language R and are available from the Bioconductor repository. application is hampered by lack of integrative tools that can be used by any experience level. To fill this gap, we developed a freely available QC and pre-processing of Affymetrix gene expression results, extending, integrating and harmonizing functionality of Bioconductor packages. The be easily accessed through a wizard-like web portal at http://www.arrayanalysis.org or downloaded for local use in R. The provides extensive documentation, including user guides, interpretation real output illustrations and detailed technical documentation. It newcomers to the field in performing state-of-the-art QC and pre- offering data analysts an integral open-source package. Providing the community with this easily accessible tool will allow improving data reuse and adoption of standards.