[BioC] Tumor and Normal samples copy number estimation with CRLMM

[Sole Acha, Xavi]

Dear all,

I want to estimate copy number values for a set of ~200 samples (100 paired Tumor and Normal mucosa). Do I need to tell CRLMM that I have "normal/germline" samples (with an expected average copy number of 2) and tumor samples (which may hay many genomic alterations). Furthermore, is it useful/do I need to specify the N-T paired design I have in my data?

I am using R 2.12.1 with CRLMM 1.8.11.

Thank you very much in advance,

Xavi.

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Xavier Solé Acha
Unitat de Biomarcadors i Susceptibilitat
Unit of Biomarkers and Susceptibility
Institut Català d'Oncologia // Catalan Institute of Oncology
Gran Via de L'Hospitalet 199-203
08908 L'Hospitalet de Llobregat, Barcelona, Spain.
Phone: +34 93 260 71 22 / +34 93 260 71 86 (ext. 7122)
Fax: +34 93 260 71 88
E-mail: x.sole (at) iconcologia.net