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)

