"Array Studio has become a very important tool for us. In our lab we are interested in finding chromosomal aberrations in different types of cancer. For that purpose we have performed different types of micro-array experiments including Affymetrix SNPs arrays, Agilent 244k and Agilent customized array. Eventually we also do Affymetrix expression arrays. Before having ArrayStudio we had to relay on the different software that could handle only one array platform and offered no much possibilities for statistical analysis. Now, we can handle different array platforms with just one software. Currently I have in ArrayStudio a project for all my SNP6.0 arrays, another project for all my Agilent 244k experiment and a project in which my CNV data from the SNP6.0 are integrated with expression data from the corresponding samples. The possibility to integrate CNV data with expression data is in my opinion one the most important feature of ArrayStudio together with the flexibility for performing statistical analysis. The flexibility is extended to the visualization and export of the results.
For the CNV analysis in cancer chromosomes we need to have a segmentation algorithm allowing us to choose the appropriate parameters or thresholds since we usually have polyploidy samples. ArrayStudio does here a good job. We perform different segmentations and save those results. Then we chose which segmentation we want to visualized and use for final result."