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. The
     annotation slot of the BSData object needs to be set correctly in
     order for the function to find the IDs of the negative control
     beads.

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

     Matrix of detection scores with the same dimensions as the exprs
     matrix of BSData. This matrix can be stored in a BSData object
     using the Detection function

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

     Mark Dunning and Andy Lynch

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

     ##BSData@annotation = "Humanv3"
     ##Detection(BSData) = calculateDetection(BSData)

