normalize              package:codelink              R Documentation

_N_o_r_m_a_l_i_z_a_t_i_o_n _w_r_a_p_p_e_r _f_o_r _C_o_d_e_l_i_n_k _o_b_j_e_c_t_s.

_D_e_s_c_r_i_p_t_i_o_n:

     Takes a Codelink object and applies normalization to intensity
     values.

_U_s_a_g_e:

         normalize(object, method = "quantiles", log.it = TRUE, preserve = FALSE,
                     weights = NULL, verbose = FALSE)

_A_r_g_u_m_e_n_t_s:

  object: an object of class "Codelink".

  method: method to use in normalization.

  log.it: logical; if data should be log2.

preserve: logical; if Ri slot should be preserved.

 weights: weights vector for method CyclicLoess.

 verbose: should informative output be printed.

_D_e_t_a_i_l_s:

     Currently supported methods include "loess", "quantiles" and
     "median".   Median normalization is analogous to the default
     method applied for the  manufacturer in the Codelink software.
     Loess is a modified version of  CyclicLoess implemented in the
     affy package, allowing missing values and  weights. Quantile
     normalization uses the normalizeQuantiles() function in the  limma
     package.

_V_a_l_u_e:

     A Codelink object with normalized intensity values.

_A_u_t_h_o_r(_s):

     Diego Diez

_E_x_a_m_p_l_e_s:

     ## Not run: 
             data(codelink.example)
             # Background correction.
             codelink.example <- bkgdCorrect(codelink.example,
             method = "half")
             # Normalization.
             codelink.example <- normalize(codelink.example,
             method = "quantile")
     ## End(Not run)

