bgAdjust                package:lumi                R Documentation

_B_a_c_k_g_r_o_u_n_d _a_d_j_u_s_t_m_e_n_t _f_o_r _I_l_l_u_m_i_n_a _d_a_t_a

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

     The method adjusts the data by subtracting an offset, which is
     estimated based on the quantile of the control probes

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

     bgAdjust(lumiBatch, probs = 0.5, ...)

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

lumiBatch: A LumiBatch object with controlData slot include control
          probe information 

   probs: The quantile used to estimate the background 

     ...: other parameters used by 'quantile' method 

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

     The method adjusts the data by subtracting an offset, which is
     estimated based on the quantile of the control probes. The control
     probe information is kept in the controlData slot of the LumiBatch
     object. If no control data information, the method will do
     nothing.

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

     It returns a LumiBatch object with background adjusted.

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

     Pan Du

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

     'lumiB'

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

             data(example.lumi)
             ## Here will assume the minimum of the control probe as the background,
             ##    because there is no negative control (blank beads) information for the Barnes data.
             example.lumi.b <- bgAdjust(example.lumi, probs=0)

