quantileNormalization        package:RNAither        R Documentation

_Q_u_a_n_t_i_l_e _n_o_r_m_a_l_i_z_a_t_i_o_n

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

     Quantile normalization (see References)

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

     quantileNormalization(header, dataset, listOfArgs)

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

  header: the header of a dataset file generated with
          'generateDatasetFile' 

 dataset: an R data frame generated with 'generateDatasetFile' 

listOfArgs: a list containing: 

          - a character string specifying the column whose values will
          be used for normalization

          - 1 or 2, 1 meaning a normalization per experiment, 2 meaning
          a normalization per plate 

_V_a_l_u_e:

     Returns a list, containing:

 header : the new header (with an added entry about the normalization
          procedure in the comments)

dataset : the new dataset with normalized values. The old values are
          saved in an extra column with the suffix ".old"

_R_e_f_e_r_e_n_c_e_s:

     B.M. Bolstad, R.A. Irizarry, M. Astrand, and T.P. Speed. A
     Comparison of Normalization Methods for High Density
     Oligonucleotide Array Data Based on Variance and Bias.
     Bioinformatics, 19(2): 185-193, 2003

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

     data(exampleHeader, package="RNAither")
     data(exampleDataset, package="RNAither")

     normres <- quantileNormalization(header, dataset, list(2, "SigIntensity"))
     newheader <- normres[[1]]
     newdataset <- normres[[2]]

