References

The fast development of high-throughput technologies enabled us to access to more than 1.5 million markers for genetic variation on a human subject at a time. Under such circumstance, the need for a unified framework to manage the data provided by experiments based on mi-croarrays and methods that would help the user analyse such big datasets in the most efficient manner has increased significantly. We developed an R/BioConductor package, oligo, struc-tured to handle all array designs by Affymetrix Inc. and NimbleGen Systems Inc. The package implements preprocessing methodologies and the genotyping algorithm CRLMM for Affymetrix SNP arrays (50K, 250K, SNP 5.0 and SNP 6.0). In this work we demonstrate the main features of the package, focusing on applications using SNP arrays. We present results that attest how CRLMM outperforms standard genotyping tools and strategies for copy number analyses usin