BASHExtended            package:beadarray            R Documentation

_B_A_S_H - _E_x_t_e_n_d_e_d _D_e_f_e_c_t _A_n_a_l_y_s_i_s

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

     Returns a score, which assesses the extent to which the background
     is changing across the array/strip.

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

     BASHExtended(BLData, array, neighbours = NULL, E = NULL, E.BG = NULL)

_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, using default 'generateNeighbours' settings.

       E: Numerical vector - The error image to use. Optional - if left
          blank, it will be computed, using 'generateE' (with 'bgfilter
          = "none"', i.e. no background filter applied).

    E.BG: Numerical vector - The background error image to use.
          Optional - if left blank, it will be computed from 'E', using
          default 'BGFilter' settings (i.e. 'method = "median"').

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

     'BASHExtended' assesses the change of background across an array.

     The error image used should not be background filtered (as opposed
     to the error image used in 'BASHDiffuse'). Here, E is the error
     image

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

     Scalar (Extended defect score)

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

     Jonathan Cairns

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

     Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkwosky and
     Marcelo O. Magnasco (2007). Harshlight: A "corrective make-up"
     program for microarray chips. R package version 1.8.0.
     http://asterion.rockefeller.edu/Harshlight/

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

     'BASH', 'generateE', 'BGFilter', 'generateNeighbours',

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

     data(BLData)
     an <- arrayNames(BLData)
     extended <- NULL

     for(i in 1:length(an))
     {
             extended[i] <- BASHExtended(BLData, i)
     }

