arrayMagic: two-colour cDNA microarray quality control and preprocessing.

arrayMagic is a software package for quality control and preprocessing of two-colour cDNA microarray data. The automated analysis pipeline comprises data import, normalization, replica merging, quality diagnostics and data export. The script-based processing combines reproducibility and flexibility at high-throughput and provides quality-assured and preprocessed microarray data to high-level follow-up analysis. The R package arrayMagic is available with BSD license at http://www.bioconductor.org a.buness@dkfz.de The package contains documentation in the form of manual pages and a vignette with a guided tour of a typical workflow.