controlNorm             package:RNAither             R Documentation

_N_o_r_m_a_l_i_z_a_t_i_o_n _o_n _c_o_n_t_r_o_l_s

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

     Performs a normalization on either positive or negative controls.

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

     controlNorm(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

          - 0 or 1, 0 meaning a normalization on the median of negative
          controls, 1 meaning a normalization on the median of positive
          controls. Can also be the ' GeneName' of a specific control
          siRNA

          - 1 or 2, 1 meaning the signal values are divided by the
          median, 2 meaning the median is subtracted from the signal
          values 

_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 <- controlNorm(header, dataset, list(2, 0, "SigIntensity", 1))

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

