divNorm               package:RNAither               R Documentation

_M_e_a_n, _m_e_d_i_a_n, ... , _n_o_r_m_a_l_i_z_a_t_i_o_n

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

     Normalization with the mean, median, or any other function.

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

     divNorm(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

          - a function to be used for the normalization, e.g. ' mean',
          ' median', ...

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

          - 1 or 2, 1 meaning the normalization is achieved by a
          division of the intensity values by the outcome of '
          funname', 2, meaning by a substraction

          - a flag specifying whether controls should be excluded for
          the computation of the result of the function specified in
          the first element (1) or not (0). 

_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" 

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

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

     normres <- divNorm(header, dataset, list(median, 2, 1, "SigIntensity", 1))

     newheader <- normres[[1]]
     newdataset <- normres[[2]]

