beadResids             package:beadarray             R Documentation

_C_a_l_c_u_l_a_t_e_s _p_e_r _s_t_r_i_p/_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:

     Calculates the per bead residuals for a given strip/array using 
     data from a 'BeadLevelList'.

_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 use in the 
          calculation of residuals.  See 'getArrayData' for a list of
          possibilities

   array: integer specifying the strip/array to use

     log: if TRUE then use log2 intensities of each bead

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

       n: numeric value defining a cut-off for the number of  median
          absolute deviations (MADs) from the median to use for 
          determining outliers.  The default value is 3.  Only used
          when  '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))

