designMatrix              package:limma              R Documentation

_C_o_n_s_t_r_u_c_t _D_e_s_i_g_n _M_a_t_r_i_x

_D_e_s_c_r_i_p_t_i_o_n:

     Construct a design matrix from the data.frame of target
     information. Currently only for two color array experiments using
     a common reference.

_U_s_a_g_e:

     designMatrix(targets, ref) 

_A_r_g_u_m_e_n_t_s:

 targets: data.frame with columns 'Cy3' and 'Cy5' specifying which RNA
          was hybridized to each array

     ref: character string giving name of reference RNA

_D_e_t_a_i_l_s:

     There is a need for design matrices for direct two-color design
     and for single-channel experiments but, this version is only for
     reference designs.

_V_a_l_u_e:

     The design matrix.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     An overview of linear model functions in limma is given by
     5.LinearModels.

_E_x_a_m_p_l_e_s:

     targets <- data.frame(Cy3=c("Ref","Control","Ref","Treatment"),Cy5=c("Control","Ref","Treatment","Ref"))
     designMatrix(targets, "Ref")

