ANDROMEDA: A MATLAB automated cDNA Microarray data analysis platform

DNA microarrays constitute a relatively new biological technology which allows gene expression profiling at a global level by measuring mRNA abundance. However, the grand complexity characterizing a microarray experiment entails the development of computationally powerful tools apt for probing the biological problem studied. ANDROMEDA (Automated aND RObust Microarray Experiment Data Analysis) is a MATLAB implemented program which performs all steps of typical microarray data analysis including noise filtering processes, background correction, data normalization, statistical selection of differentially expressed genes based on parametric or non parametric statistics and hierarchical cluster analysis resulting in detailed lists of differentially expressed genes and formed clusters through a strictly defined automated workflow. Along with the completely automated procedure, ANDROMEDA offers a variety of visualization options (MA plots, boxplots, clustering images etc). Emphasis is given to the output data format which contains a substantial amount of useful information and can be easily imported in a spreadsheet supporting software or incorporated in a relational database for further processing and data mining.