rg.series.spot             package:limma             R Documentation

_R_e_a_d _R_G_L_i_s_t _f_r_o_m _S_P_O_T _I_m_a_g_e _A_n_a_l_y_s_i_s _O_u_t_p_u_t _F_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Extracts an RGList from a series of Spot image analysis files.
     This is a depreciated function. Use 'read.maimages' instead.

_U_s_a_g_e:

     rg.series.spot(slides,path=NULL,names.slides=names(slides),suffix="spot",wt.fun=NULL,verbose=TRUE,...)

_A_r_g_u_m_e_n_t_s:

  slides: character vector giving the names of the files containing the
          Spot output

    path: character string giving the directory containing the files.
          Can be omitted if the files are in the current working
          directory.

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

  suffix: the file names are assumed to have this suffix added to names
          in 'slides'

  wt.fun: function to calculate quality weights

 verbose: 'TRUE' to report each time a file in read in

     ...: any other arguments to be passed to 'scan'

_D_e_t_a_i_l_s:

     This function extracts the foreground and background intensities
     from a series of files, produced by the image analysis program
     SPOT, and assembles them in the components of one list.

     Spot quality weights may also be extracted using an optional
     weight function.

_V_a_l_u_e:

     A list containing the components 

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

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

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

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

 weights: spot quality weights, if 'wt.fun' is not 'NULL'

_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.

