findAllOutliers          package:beadarray          R Documentation

_F_i_n_d _o_u_t_l_i_e_r_s _o_n _a_r_r_a_y

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

     Function to find all beads which are outliers for their particular
     bead type on a given array.

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

     findAllOutliers(BLData, array, log=FALSE, n=3, ignoreList=NULL)

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

  BLData: an BeadLevelList object containing bead level data

   array: numeric value specifying which array we want to find outliers
          on

     log: if TRUE the log2 intensities will be used to calculate
          outliers

       n: Specify a cut-off for outliers as n median absolute
          deviations from the mean. The default value is 3

ignoreList: list of ProbeIDs to be omitted from the averaging
          procedure. These could be Illumina internal controls which
          are replicated many thousands of times on arrays

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

     We find the outliers for each bead type on the array in turn using
     the 'findBeadStatus' function and keep a list of the outliers
     found. By default, outliers for a particular bead type are
     determined using a 3 MAD cut-off from the mean.

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

     numeric vector giving a row index from the BeadLevelList for all
     the beads that are outliers for their bead type.

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

     Mark Dunning and Mike Smith

_S_e_e _A_l_s_o:

     'findBeadStatus'

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

     data(BLData)

     length(findAllOutliers(BLData, 1))

     length(findAllOutliers(BLData, 1, log=TRUE))

     length(findAllOutliers(BLData, 1, n=5))

