lumiB                  package:lumi                  R Documentation

_B_a_c_k_g_r_o_u_n_d _c_o_r_r_e_c_t_i_o_n _o_f _I_l_l_u_m_i_n_a _d_a_t_a

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

     Background correction of Illumina data

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

     lumiB(lumiBatch, method = c('forcePositive', 'none', 'bg.adjust'), ...)

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

lumiBatch: a LumiBatch Object, which can be the return of 'lumiR' 

  method: the background correction method, it can be any function with
          a LumiBatch Object as the first argument and return a
          LumiBatch Object 

     ...: other parameters used by the user provided background
          correction method  

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

     The default background correction method ('forcePositive') will
     force all expression values to be positive by adding an offset
     (minus minimum value plus one), it does nothing if all expression
     values are positive. 'none' does not but return the lumiBatch
     object. 'bg.adjust' method is based on the 'bg.adjust' function in
     affy package. User can also provide their own function with a
     LumiBatch Object as the first argument and return a LumiBatch
     Object with background corrected.

     Thanks Kevin Coombes (M.D. Anderson Cancer Center) suggested
     adding this function.

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

     return a LumiBatch Object with background corrected.

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

     Pan Du, Kevin Coombes

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

     'lumiExpresso'

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

     ## load example data
     data(example.lumi)

     ## Do the default background correction method
     lumi.B <- lumiB(example.lumi)

