varAdjust              package:RNAither              R Documentation

_V_a_r_i_a_n_c_e _a_d_j_u_s_t_m_e_n_t

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

     Divides the intensity values by their median absolute deviation
     (of the experiment or of the plate)

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

     varAdjust(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 screen, 2 a
          normalization per plate

          - a flag specifying whether controls should be excluded for
          the computation of the median absolute deviation (1) or not
          (0). 

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

     Divides the intensity values by their median absolute deviation
     (of the experiment or of the plate).

     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 of the dataset with the suffix
          ".old" 

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

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

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

