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Research Article

Discovering Subgroups of Patients from DNA Copy Number Data Using NMF on Compacted Matrices

  • Cassio P. de Campos mail,

    cassio@idsia.ch

    Affiliations: Dalle Molle Institute for Artificial Intelligence (IDSIA), Manno, Switzerland, Lymphoma and Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland

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  • Paola M. V. Rancoita,

    Affiliations: Dalle Molle Institute for Artificial Intelligence (IDSIA), Manno, Switzerland, Lymphoma and Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland, University Centre of Statistics for Biomedical Sciences (CUSSB), Vita-Salute San Raffaele University, Milan, Italy

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  • Ivo Kwee,

    Affiliations: Dalle Molle Institute for Artificial Intelligence (IDSIA), Manno, Switzerland, Lymphoma and Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland

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  • Emanuele Zucca,

    Affiliation: Lymphoma Unit, Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland

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  • Marco Zaffalon,

    Affiliation: Dalle Molle Institute for Artificial Intelligence (IDSIA), Manno, Switzerland

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  • Francesco Bertoni

    Affiliations: Lymphoma and Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland, Lymphoma Unit, Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland

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  • Published: November 20, 2013
  • DOI: 10.1371/journal.pone.0079720

About the Authors

Cassio P. de Campos, Paola M. V. Rancoita, Ivo Kwee, Marco Zaffalon
Dalle Molle Institute for Artificial Intelligence (IDSIA), Manno, Switzerland
Cassio P. de Campos, Paola M. V. Rancoita, Ivo Kwee, Francesco Bertoni
Lymphoma and Genomics Research Program, Institute of Oncology Research (IOR), Bellinzona, Switzerland
Paola M. V. Rancoita
University Centre of Statistics for Biomedical Sciences (CUSSB), Vita-Salute San Raffaele University, Milan, Italy
Ivo Kwee
Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
Emanuele Zucca, Francesco Bertoni
Lymphoma Unit, Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland

Corresponding Author

Email: cassio@idsia.ch

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: CPdC PMVR IK MZ. Performed the experiments: CPdC PMVR IK FB. Analyzed the data: CPdC PMVR IK EZ MZ FB. Contributed reagents/materials/analysis tools: EZ FB. Wrote the paper: CPdC PMVR FB. Acquired data sets: PMVR EZ FB. Designed software tools used in the analysis: CPdC PMVR IK. Revised the manuscript critically: IK EZ MZ.