globalQuality          package:arrayQuality          R Documentation

_Q_u_a_l_i_t_y _m_e_a_s_u_r_e_s _f_o_r _g_e_n_e_r_a_l _h_y_b_r_i_d_i_z_a_t_i_o_n.

_D_e_s_c_r_i_p_t_i_o_n:

     This function provides Quality Control measures for GenePix, Spot
     and Agilent format files. It is used to create a table of measures
     to be used as reference in gpQuality, spotQuality or agQuality.

_U_s_a_g_e:

     globalQuality(fnames = NULL, path = ".", organism = c("Mm", "Hs"),
     output = FALSE, resdir = ".", DEBUG = FALSE, inputsource = "readGPR",...)

_A_r_g_u_m_e_n_t_s:

  fnames: A "character" string naming the input files.

    path: a "character" string representing the data directory.  By
          default this is set to the current working directory (".").

organism: A "character" string naming the organism genome printed on
          the array, either "Mm" or "Hs". By default, organism is set
          to "Mm". It is used to retrieve the corresponding reference
          tables.

  output: Logical. If 'TRUE', the quality measures are printed to a
          file. 

  resdir: A "character" string representing the directory where the
          results will be saved. By default, this is set to the current
          working directory ("."). 

   DEBUG: If 'TRUE', debug statements are printed.

inputsource: A "character" string providing the name of the function to
          use to read the input files. It should be inputsource =
          "readGPR" for GenePix format files, inputsource = "readSpot"
          for Spot files, or inputsource = "readAgilent" for Agilent
          format. By default, 'inputsource' is set to "readGPR".

     ...: additional arguments

_V_a_l_u_e:

     A matrix of Quality Control measures, each column representing a
     different input slide.

_A_u_t_h_o_r(_s):

     Agnes Paquet

_S_e_e _A_l_s_o:

     'gpQuality', 'slideQuality', 'MmReferenceDB', 'readGPR',
     'readSpot', 'readAgilent'

_E_x_a_m_p_l_e_s:

     datadir <- system.file("gprQCData", package="arrayQuality")
     if (interactive())
     reference <- globalQuality(fnames="9Mm137.gpr", path=datadir, organism="Mm")

