findHighestSD           package:beadarray           R Documentation

_H_i_g_h_e_s_t _s_t_a_n_d_a_r_d _d_e_v_i_a_t_i_o_n.

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

     Function for finding which bead types on a particular array have
     the standard deviation of their intensities greater than some
     limit.

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

     findHighestSD(BLData, array, limit = 1)

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

  BLData: BeadLevelList object containing bead level data

   array: numeric value for the array that we want to use

   limit: threshold value for the standard deviation of beads

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

     The standard deviation for bead intensities of each bead type is
     calculated in turn and if this value exceeds the defined limit
     then we add the  ProbeID of the bead type to a list which we
     return.

     The standard deviation that we calculate is based on the log2 bead
     intensities.

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

     numeric vector giving the ProbeIDs which were calculated to have
     standard deviation greater than 'limit'.

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

     Mark Dunning

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

     data(BLData)

     ##Default is to find bead types with standard deviation of intensity > 1

     findHighestSD(BLData, 1)

     ##limit can be changed eg. to give ProbeIDs with standard deviation > 0.7

     findHighestSD(BLData, 1, limit=0.7)

     ##Any ProbeIDs can be examined in more detail

     plotBeadIntensities(BLData, 678,1)

     probeDiagnostics(BLData, 678, 1)

