beadResids             package:beadarray             R Documentation

_C_a_l_c_u_l_a_t_e_s _p_e_r _a_r_r_a_y _b_e_a_d-_l_e_v_e_l _r_e_s_i_d_u_a_l_s

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

     Retrieves the per bead data stored in a 'BeadLevelList' object for
     a given array.  In the case of the log-ratios or average
     log-intensities, these values are calculated for each bead.

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

     beadResids(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 which intensities to obtain.
          Possibilities are '"G"' (single channel data) and '"R"'
          (two-colour data)

   array: numeric value giving the array we are interested in

     log: if TRUE then use log2 intensities of each bead

  method: chracter string specifying the summarisation method  (see
          help page for 'createBeadSummaryData' for further details).

       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"' (see
          'createBeadSummaryData' help page for further details).

    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:

     Calculates the residuals, i.e. the differences between the summary
     values obtained from 'createBeadSummaryData' and the individual
     values for each bead.

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

     A vector containing the residual values.

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

     Matt Ritchie

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

     data(BLData)
     summary(beadResids(BLData, log=TRUE))

