cmat                  package:daMA                  R Documentation

_C_o_n_t_r_a_s_t _m_a_t_r_i_x _d_e_s_c_r_i_b_i_n_g _t_h_e _e_x_p_e_r_i_m_e_n_t_a_l _q_u_e_s_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     This matrix of numerical constants describes the experimental
     question, p say. Each experimental question is described by a
     single contrast vector (a single row in cmat) or by a contrast
     matrix (several rows in cmat). The ordering of the columns
     corresponds to that of the associated design matrix X. Thus,
     typically the first two elements in a row of cmat are reserved for
     for the two dyes. E.g. to compare the two dyes, we set (-1, 1, 0,
     ..., 0).

_U_s_a_g_e:

     data(cmat)

_R_e_f_e_r_e_n_c_e_s:

     Bretz, F and Landgrebe J and Brunner E (2003):"Design and analysis
     of two colour factorial microarray experiments", submitted.

_E_x_a_m_p_l_e_s:

     data(cmat)
     ## maybe str(cmat) ; plot(cmat) ...

