normalize.quantiles.target  package:preprocessCore  R Documentation

_Q_u_a_n_t_i_l_e _N_o_r_m_a_l_i_z_a_t_i_o_n _u_s_i_n_g _a _s_p_e_c_i_f_i_e_d _t_a_r_g_e_t _d_i_s_t_r_i_b_u_t_i_o_n _v_e_c_t_o_r

_D_e_s_c_r_i_p_t_i_o_n:

     Using a normalization based upon quantiles, these function
     normalizes the columns of a matrix based upon a specified
     normalization distribution

_U_s_a_g_e:

       normalize.quantiles.use.target(x,target,copy=TRUE)
       normalize.quantiles.determine.target(x,target.length=NULL)

_A_r_g_u_m_e_n_t_s:

       x: A matrix of intensities where each column corresponds to a
          chip and each row is a probe.

    copy: Make a copy of matrix before normalizing. Usually safer to
          work with a copy

  target: A vector containing datapoints from the distribution to be
          normalized to

target.length: number of datapoints to return in target distribution
          vector. If 'NULL' then this will be taken to be equal to the
          number of rows in the matrix.

_D_e_t_a_i_l_s:

     This method is based upon the concept of a quantile-quantile plot
     extended to n dimensions. No special allowances are made for
     outliers. If you make use of quantile normalization either through
     'rma' or 'expresso' please cite Bolstad et al, Bioinformatics
     (2003).

     These functions will handle missing data (ie NA values), based on
     the assumption that the data is missing at random.

_V_a_l_u_e:

     From 'normalize.quantiles.use.target' a normalized 'matrix'.

_A_u_t_h_o_r(_s):

     Ben Bolstad, bmb@bmbolstad.com

_R_e_f_e_r_e_n_c_e_s:

     Bolstad, B (2001) _Probe Level Quantile Normalization of High
     Density Oligonucleotide Array Data_. Unpublished manuscript <URL:
     http://bmbolstad.com/stuff/qnorm.pdf>

     Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P.
     (2003) _A Comparison of Normalization Methods for High Density
     Oligonucleotide Array Data Based on Bias and Variance._
     Bioinformatics 19(2) ,pp 185-193. <URL:
     http://bmbolstad.com/misc/normalize/normalize.html>

_S_e_e _A_l_s_o:

     'normalize'