designI2M               package:limma               R Documentation

_C_o_n_v_e_r_t _I_n_d_i_v_i_d_u_a_l _C_h_a_n_n_e_l _D_e_s_i_g_n _M_a_t_r_i_x _t_o _M-_A _F_o_r_m_a_t

_D_e_s_c_r_i_p_t_i_o_n:

     Convert a design matrix in terms of individual channels to ones in
     terms of M-values or A-values for two-color microarray data.

_U_s_a_g_e:

     designI2M(design)
     designI2A(design)

_A_r_g_u_m_e_n_t_s:

  design: numeric model matrix with one row for each channel
          observation, i.e., twice as many rows as arrays

_D_e_t_a_i_l_s:

     If 'design' is a model matrix suitable for modelling individual
     log-intensities for two color microarray data, then 'designI2M'
     computes the corresponding model matrix for modelling M-values
     (log-ratios) and 'designI2A' computes the model matrix for
     modelling A-values (average log-intensities).

     Note that the matrices 'designI2M(design)' or 'designI2A(design)'
     may be singular if not all of the coefficients are estimable from
     the M or A-values. In that case there will be columns containing
     entirely zeros.

_V_a_l_u_e:

     numeric model matrix with half as many rows as 'design'

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     'model.matrix' in the stats package.

     An overview of individual channel linear model functions in limma
     is given by 07.SingleChannel.

_E_x_a_m_p_l_e_s:

     X <- cbind(1,c(1,1,1,1,0,0,0,0),c(0,0,0,0,1,1,1,1))
     designI2M(X)
     designI2A(X)