getArrayData            package:beadarray            R Documentation

_G_e_t_s _t_h_e _r_a_w _d_a_t_a _f_r_o_m _a _B_e_a_d_L_e_v_e_l_L_i_s_t _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     Retrieves the per bead data from a 'BeadLevelList' object  for a
     given array.

_U_s_a_g_e:

     getArrayData(BLData, what="G", array=1,log=TRUE, method="illumina", n=3, trim=0.05)

_A_r_g_u_m_e_n_t_s:

  BLData: 'BeadLevelList'

    what: character string specifying the values to retrieve.
          Possibilities are '"ProbeID"', '"GrnX"', '"GrnY"', '"G"',
          '"Gb"' for single channel data and '"R"', '"Rb"', '"residR"',
          '"residG"', '"M"' (log-ratios) '"residM"' or '"A"' (average
          log-intensities) for two-colour data

   array: numeric value giving the array we are interested in

     log: if TRUE log2 of the raw intensities are returned

  method: chracter string specifying the summarisation method to use in
          'createBeadSummaryData' (see help page for further details).
          Only used when 'what="residR"', '"residG"' or '"residM"'.

       n: use n median absolute deviations from the median as a cut-off
          for outliers. Only used when 'what="residR"', '"residG"' or
          '"residM"' and 'method="illumina"'.

    trim: fraction of intensities to remove from the bead summary
          calculations when 'method="trim"', or the fraction of
          intensities to set to the 'trim' and 1-'trim' percentile
          intensities when 'method="winsorize"'.  Default value is
          0.05. Only used when 'what="residR"', '"residG"' or
          '"residM"'.

_D_e_t_a_i_l_s:

     'getArrayData' retrieves the raw per bead data from a given array.
      The data is either stored in 'BeadLevelList' object (e.g.
     '"ProbeID"', '"GrnX"', '"GrnY"', '"G"', '"Gb"', '"R"' and '"Rb"'
     or calculated from these values (e.g. '"residR"', '"residG"',
     '"M"', '"residM"' or '"A"').  When 'log=TRUE', intensity data is
     returned on the log2 scale.

_V_a_l_u_e:

     A vector containing the raw bead data (or residuals) for a
     particular array.

_A_u_t_h_o_r(_s):

     Matt Ritchie

_E_x_a_m_p_l_e_s:

     data(BLData)
     summary(getArrayData(BLData))

