findMostOutliers          package:beadarray          R Documentation

_B_e_a_d_s _w_i_t_h _m_o_s_t _o_u_t_l_i_e_r_s

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

     Function to find out which bead types on a particular array have
     the most outliers

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

     findMostOutliers(BLData, array, limit = 5)

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

  BLData: an BeadLevelList object containing bead level data

   array: numeric value giving the number of the array we want to find
          outliers for

   limit: numeric value giving the limit for the number of outliers
          (default is 5)

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

     Takes each bead type found on the array in turn and calculates the
     number of outliers found for the bead type. If more than 'limit'
     outliers are found for a bead type we add the ProbeID to a list.
     Preliminary investigation suggests that bead types rarely have
     more than 5 outliers.

     This function uses the default method of finding outliers using 3
     median absolute deviations from the bead mean with raw (un-logged
     data).

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

     vector of numeric values giving the ProbeIDs of bead types which
     have more than 'limit' number of outliers.

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

     Mark Dunning

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

     'findBeadStatus'

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

     data(BLData)

     ##Default is to find bead types with more than 5 outliers

     findMostOutliers(BLData, 1)

     ##Can change limit parameter to find all bead types with more than 3 outliers (say)

     findMostOutliers(BLData, 1, limit=3)

     ##ProbeIDs returned by function can be investigated in more detail

     plotBeadIntensities(BLData, 807, 1)

