ArticleScientific reports2016
Rawcopy: Improved copy number analysis with Affymetrix arrays.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- Clinically relevant treatment of PDX models reveals patterns of neuroblastoma chemoresistance.Science advances · 2022Article
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- Clinical and molecular findings in three Japanese patients with N-acetylneuraminic acid synthetase-congenital disorder of glycosylation (NANS-CDG).Scientific reports · 2022Article
- The diagnostic utility of DNA copy number analysis of core needle biopsies from soft tissue and bone tumors.Laboratory investigation; a journal of technical methods and pathology · 2022Article
- Genetic alterations associated with malignant transformation of sporadic vestibular schwannoma.Acta neurochirurgica · 2022Article
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- Lipid-Producing Ciliochoroidal Melanoma with Expression of HMG-CoA Reductase.Ocular oncology and pathology · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
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