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. ------ Xavier Sol? Acha Unitat de Biomarcadors i Susceptibilitat Unit of Biomarkers and Susceptibility Institut Catal? 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