calcbackground          package:phyloarray          R Documentation

_C_a_l_c_u_l_a_t_e _b_a_c_k_g_r_o_u_n_d

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

     Background values are calculated based on empty spots. The values
     for non-empty spots are calculated by an interpolation procedure.

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

       calcbackground(datalist, emptyfield="empty")

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

datalist: An object of type 'phyloarray'

emptyfield: ID of the spots which are empty, i.e. the spots that are
          used for background calculation or spots which shouldn't give
          any signal.

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

     The function calculates the background using an kriging algorithm.
     It is important to note that only the spots with 'ID==emptyfield'
     are used and that badspots, i.e. spots with a sd/signal<cutoff are
     removed from background calculation.

     Other or more flexible interpolation procedures might be included
     in future versions.

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

     The function returns the same object as given in 'datalist', but
     the 'Gb' and 'Rb' values are replaced by the calculated background
     values.

_N_o_t_e:

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

     Kurt Sys (kurt.sys@advalvas.be)

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

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

     'Scandataraw' 'Phylodata'

     'init.data'

     'plotbackground'

     'krige'

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

       # load data this-is-escaped-codenormal-bracket33bracket-normal, i.e. this-is-escaped-codenormal-bracket34bracket-normal
       data(Phylodata)

       # histogram of background values before interpolation procedure
       hist(scans$R[,"40"], nclass=50)

       scans <- calcbackground(scans)

       # histogram of background values after interpolation procedure
       hist(scans$R[,"40"], nclass=50)

