rg.quantarray             package:limma             R Documentation

_E_x_t_r_a_c_t _R_G_L_i_s_t _f_r_o_m _d_a_t_a._f_r_a_m_e_s _C_o_n_t_a_i_n_i_n_g _Q_u_a_n_t_a_r_r_a_y _D_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     Extracts an RGList from Quantarray image analysis output when the
     data has already been read from files into data.frames objects.

_U_s_a_g_e:

     rg.quantarray(slides,names.slides=names(slides),suffix="qta")

_A_r_g_u_m_e_n_t_s:

  slides: Character vector giving the names of the data frames
          containing the Spot output.

names.slides: Names to be associated with each slide as column name.

  suffix: The dataframe names are assumed to have this suffix added to
          names in 'slides'.

_D_e_t_a_i_l_s:

     This function extracts the foreground and background intensities
     from a series of data frames and assembles them in the components
     of one list.

_V_a_l_u_e:

     A list containing the components 

       R: A matrix containing the red channel foreground intensities
          for each spot for each array.

      Rb: A matrix containing the red channel background intensities
          for each spot for each array.

       G: A matrix containing the green channel foreground intensities
          for each spot for each array.

      Gb: A matrix containing the green channel background intensities
          for each spot for each array.

_A_u_t_h_o_r(_s):

     Gordon Smyth

_S_e_e _A_l_s_o:

     An overview of LIMMA functions for reading data is given in
     3.ReadingData.

