outlierPlot            package:beadarray            R Documentation

_L_o_c_a_t_i_o_n_s _o_f _o_u_t_l_i_e_r_s _o_n _a_n _I_l_l_u_m_i_n_a _c_h_i_p

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

     Diagnostic function that reports how many outliers are found on a
     specific array on a chip. We take advantage of the segmental
     structure of the array and break-down the number of outliers into
     9 sections.

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

     outlierPlot(BLData, array = array, log = FALSE, plot = FALSE)

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

  BLData: A BeadLevelList object containing the bead-level data for an
          Illumina experiment

   array: The number of the array of interest

     log: if TRUE calculate outliers on the log2 scale.  If FALSE
          calculate outliers on the original scale

    plot: if TRUE a diagnostic plot will be produced, otherwise only
          the numbers of outliers will be returned.

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

     The number of outliers are computed for the whole array using the
     Illumina default method that specifies a cut-off of 3 MADs from
     the median on either the log2 or original scale. These outliers
     are then split into 9 different sections on the array (the
     separation between these sections can usually be seen in the
     plots).

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

     Mark Dunning

