Rawcopy: Improved copy number analysis with Affymetrix arrays.

Mayrhofer M, Viklund B, Isaksson A

Sci Rep 6 (-) 36158 [2016-10-31; online 2016-10-31]
PubMed: 27796336 DOI: 10.1038/srep36158 Crossref: 10.1038/srep36158

Microarray data is subject to noise and systematic variation that negatively affects the resolution of copy number analysis. We describe Rawcopy, an R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP 6.0 microarray raw intensities (CEL files). Noise characteristics of a large number of reference samples are used to estimate log ratio and B-allele frequency for total and allele-specific copy number analysis. Rawcopy achieves better signal-to-noise ratio and higher proportion of validated alterations than commonly used free and proprietary alternatives. In addition, Rawcopy visualizes each microarray sample for assessment of technical quality, patient identity and genome-wide absolute copy number states. Software and instructions are available at http://rawcopy.org.

Array and Analysis Facility [Technology development]