normalize.scaling          package:affyPLM          R Documentation

_S_c_a_l_i_n_g _n_o_r_m_a_l_i_z_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Allows the user to apply scaling normalization.

_U_s_a_g_e:

     normalize.scaling(X,trim=0.02,baseline=-1,log.scalefactors=FALSE)
     normalize.AffyBatch.scaling(abatch,type=c("together","pmonly","mmonly","separate"),trim=0.02,baseline=-1,log.scalefactors=FALSE)

_A_r_g_u_m_e_n_t_s:

       X: A matrix. The columns of which are to be normalized.

  abatch: An 'AffyBatch'

    type: A parameter controlling how normalization is applied to the
          Affybatch.

    trim: How much to trim from the top and bottom before computing the
          mean when using the scaling normalization.

baseline: Index of array to use as baseline, negative values
          (-1,-2,-3,-4) control different baseline selection methods.

log.scalefactors: Compute the scale factors based on log2 transformed
          data.

_D_e_t_a_i_l_s:

     These function carries out scaling normalization of expression
     values.

_V_a_l_u_e:

     A normalized 'ExpressionSet'.

_A_u_t_h_o_r(_s):

     Ben Bolstad, bmb@bmbolstad.com

_S_e_e _A_l_s_o:

     'normalize'

_E_x_a_m_p_l_e_s:

     if (require(affydata)) {
       data(Dilution)
       normalize.AffyBatch.scaling(Dilution)
     }

