HULKResids             package:beadarray             R Documentation

_H_U_L_K - _R_e_s_i_d_u_a_l_s

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

     Calculates an set of weighted average residuals, one for each
     probe, based on the residuals of the surrounding probes.

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

     HULKResids(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:

     HULKResids calculates a weighted average residual for each probe
     on the specified array of BLData.  It makes use of the same
     neighbourhood calculations as other BASH functions.  The average
     residuals are 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.  It is intended that 'HULKResids' be
     called through 'HULK', but it is quite possible to call it as a
     stand alone function.

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

     A vector containing an average residual for each bead on the
     specified array of BLData.

_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:

     'HULK', 'BASH'

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

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

