calculateDetection         package:beadarray         R Documentation

_C_a_l_c_u_l_a_t_e _d_e_t_e_c_t_i_o_n _s_c_o_r_e_s

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

     Function to calculate detection scores for summarized data if they
     are not available.

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

     calculateDetection(BSData)

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

  BSData: An ExpressionSetIllumina object

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

     The function implements Illumina's method for calculating the
     detection scores for all bead types on a given array.  Within an
     array, Illumina discard negative control bead-types whose summary
     values are more than three MADs from the median for the negative
     controls. Illumina then rank the summarized intensity for each
     other bead-type against the summarized values for the remaining
     negative control bead-types and calculate a detection p-value 
     1-R/N, where R is the relative rank of the bead intensity when
     compared to the $N$ remaining negative controls. Thus, if a
     particular bead has higher intensity than all the negative
     controls it will be assigned a value of 0.  This calculation is
     repeated for all arrays stored in the BSData object.

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

     A modified version of BSData is returned with the detection slot
     filled with the newly created scores.

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

     Mark Dunning and Andy Lynch

