Rawcopy: Improved copy number analysis with Affymetrix arrays

Markus Mayrhofer; Björn Viklund; Anders Isaksson

doi:10.1038/srep36158

Rawcopy: Improved copy number analysis with Affymetrix arrays

Sci Rep. 2016 Oct 31:6:36158. doi: 10.1038/srep36158.

Authors

Markus Mayrhofer^{1

2}, Björn Viklund¹, Anders Isaksson¹

Affiliations

¹ Science for Life Laboratory, Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden.
² Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Nobels Väg 12A, SE-17177, Stockholm, Sweden.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't