lowessNorm             package:RNAither             R Documentation

_L_o_w_e_s_s _n_o_r_m_a_l_i_z_a_t_i_o_n

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

     Performs a plate-wise lowess normalization of the data.

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

     lowessNorm(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 used as channel 1
          (colname4ch1)

          - a character string specifying the column used as channel 2
          (colname4ch2)

          - optionally: the smoother span (smSpan) of the lowess
          function. This gives the proportion of points which influence
          the smooth at each value. Larger values give more smoothness.
          Defaults to 2/3. 

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

     Corrects intensity values in case the values of ch2 decrease with
     the increase of ch1 values.

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

