normalize-methods            package:affy            R Documentation

_N_o_r_m_a_l_i_z_e _A_f_f_y_m_e_t_r_i_x _P_r_o_b_e _L_e_v_e_l _D_a_t_a - _m_e_t_h_o_d_s

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

     Method for normalizing Affymetrix Probe Level Data

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

     normalize.methods(object)

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

  object: An 'AffyBatch'.

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

     If 'object' is an 'AffyBatch' then 'normalize(object)' returns an
     'AffyBatch' with the intensities normalized using the methodology
     specified by 'getOption("BioC")$affy$normalize.method'. The affy
     package default is 'quantiles'.

     Other methodologies can be used by specifying them with the
     'method' argument. For example to use the invariant set
     methodology described by Li and Wong (2001) one would type:
     'normalize(object, method="invariantset")'.

     Further arguments passed by '...', apart from 'method',  are
     passed along to the  function responsible for the methodology
     defined by the 'method' argument. 

     A character vector of _nicknames_ for the  methodologies available
     is returned by 'normalize.methods(object))', where 'object'  is an
      'AffyBatch', or simply by typing 'normalize.AffyBatch.methods'.
     If the nickname of a method is called "loess", the help page for
     that  specific methodology can be accessed by typing
     '?normalize.loess'. 

     For more on the normalization methodologies currently implemented
     please refer to the vignette `Custom Processing Methods'.

     To add your own normalization procedures please refer to the
     customMethods vignette.

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

     'AffyBatch-class', 'normalize'.

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

     data(affybatch.example)
     normalize.methods(affybatch.example)

