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(x.lumi, method = c('none', 'bgAdjust', 'forcePositive', 'bgAdjust.affy'), verbose = TRUE, ...)

_A_r_g_u_m_e_n_t_s:

  x.lumi: an ExpressionSet inherited object or a data matrix with
          columns as samples and rows as genes. For 'bgAdjust' method,
          it should be a LumiBatch Object 

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

 verbose: a boolean to decide whether to print out some messages 

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

_D_e_t_a_i_l_s:

     We assume the BeadStudio output data is background corrected. So
     by default, it will do nothing. The 'bgAdjust' method will
     estimate the background based on the control probe information,
     which is kept in the controlData slot of LumiBatch object. The
     'forcePositive' method 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. The purpose of
     this is to avoid NA when do logarithm transformation. 'none' does
     not but return the LumiBatch object. 'bgAdjust.affy' will call 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 an object with background corrected. The class of the
     return object is the same as the input object x.lumi.

_A_u_t_h_o_r(_s):

     Pan Du, Kevin Coombes

_S_e_e _A_l_s_o:

     'bgAdjust', '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, method='bgAdjust', probs=0)

