This investigation aims to exemplify preliminary processing, input automation, normalization, and graphical diagnosis of cDNA microarray data using Bioconductor R software packages. The packages are applied to an example of multi-slide cDNA microarray data comparing brain region tissue samples of experimental and control mice. It is shown that Bioconductor packages effectively facilitate object-oriented processing of cDNA microarray data, automate data input, and eliminate experimental artifacts of microarrays. The output objects and normalized data are ready for higher-level analysis.