HULK                package:beadarray                R Documentation

_H_U_L_K - _B_e_a_d _A_r_r_a_y _N_o_r_m_a_l_i_z_a_t_i_o_n _b_y _N_E_i_g_h_b_o_u_r_h_o_o_d _R_e_s_i_d_u_a_l_s

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

     Normalizes an probe intensities by calculating a weighted average
     residual based on the residuals of the surrounding probes.

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

     HULK(BLData, array, neighbours = NULL, invasions = 20, what = "G")

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

  BLData: 'BeadLevelList'

   array: integer specifying which strip/array to plot

neighbours: A Neighbours matrix. Optional - if left NULL, it will be
          computed.

invasions: Integer - Number of invasions used when identifying
          neighbouring beads.

    what: Specify the data in the BLData to create the residuals from. 
          Defaults to the foreground intensities of the green channel.

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

     HULK is a method of intensity normalization based upon the BASH
     framework.  Firstly For each bead a local neighbourhood of beads
     is determined, using the same process as the other BASH functions.

     For each bead a weighted average residual is calculated.  The
     average residual is calculated as the sum of the residuals for
     each bead in the neighbourhood, divided by 1 plus the number of
     invasions it took to reach that bead.  This calculation is made by
     a call to 'HULKResids'.

     The average residuals are then subtracted from each bead and the
     resulting 'BeadLevelList' object is returned.

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

     An object of class 'BeadLevelList'

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

     Mike Smith

_R_e_f_e_r_e_n_c_e_s:

     Cairns JM, Dunning MJ, Ritchie ME, Russell R, Lynch AG. (2008).
     BASH: a tool for managing BeadArray spatial artefacts.
     Bioinformatics, 24(24):2921-2.

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

     'HULKResids', 'BASH'

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

     data(BLData)
     o <- HULK(BLData, 1)

