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ITALICS | An algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays

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A package based on a normalization method that estimates both biological and nonrelevant effects in an alternate, iterative manner, accurately eliminating irrelevant effects. ITALICS uses a normalization algorithm for Affymetrix SNP arrays. This method was designed for the normalization and analysis of DNA copy number and significantly outperformed other methods, such as CNAT 3.0, CNAT 4.0, CNAG and GIM, in terms of SNR and can also be used to correct for experimental artifacts due to spatial effects. This method was validated by QPCR and accurately detected the breakpoints in genomic profiles. It could therefore be used to improve the characterization of samples in genomic studies.

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ITALICS forum

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ITALICS classification

ITALICS specifications

Unique identifier:
OMICS_02064
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Stability:
Stable
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Maintained:
Yes

ITALICS distribution

versioning

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No versioning.

ITALICS support

Documentation

Credits

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Publications

Institution(s)

Institut Curie, Service de Bioinformatique, INSERM, U900, CNRS UMR144, Institut Curie, Translational Research Department, Paris, France

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