rg.spot                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 _S_P_O_T _D_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

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

_U_s_a_g_e:

     rg.spot(slides,names.slides=names(slides),suffix="spot",area=FALSE)

_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'.

    area: If 'TRUE' then the output list includes a component
          containing the spot areas.

_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.

     Spot areas may also be extracted, which is useful for
     downweighting unusually small or large spots in subsequent
     analyses.

_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.

