TY - JOUR T1 - Rawcopy: Improved copy number analysis with Affymetrix arrays JF - bioRxiv DO - 10.1101/027409 SP - 027409 AU - Markus Mayrhofer AU - Björn Viklund AU - Anders Isaksson Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/10/22/027409.abstract N2 - Rawcopy is an R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP 6.0 microarray raw intensities (CEL files). It uses data from a large number of reference samples to produce log ratio for total copy number analysis and B-allele frequency for allele-specific copy number and heterozygosity analysis. Rawcopy achieves higher signal-to-noise ratio than commonly used free and proprietary alternatives, leading to improved identification of copy number alterations. In addition, Rawcopy visualises each microarray sample for assessment of technical quality, patient identity and genome-wide absolute copy number states. ER -