getArrayData            package:beadarray            R Documentation

_G_e_t _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 raw bead data from a 'BeadLevelList' object  for a
     given strip/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"', '"A"' (average
          log-intensities) and '"beta"'  (=R/(R+G)) for two-colour data

   array: integer specifying the strip/array to use

     log: if TRUE log2 of the raw intensities are returned (ignored if
          'what="beta"')

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

       n: numeric value specifying the number of median absolute
          deviations (MADs) from the median to use 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 bead data from a given array. 
     The data is either extracted from a 'BeadLevelList' object (e.g.
     '"ProbeID"', '"GrnX"', '"GrnY"', '"G"', '"Gb"', '"R"' and '"Rb"'
     or calculated from these values (e.g. '"residR"', '"residG"',
     '"M"', '"residM"', '"A"' or '"beta"'). 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))

