subtractBackground         package:RNAither         R Documentation

_B_a_c_k_g_r_o_u_n_d _s_u_b_s_t_r_a_c_t_i_o_n

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

     Substracts a specified background value from the intensity values.

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

     subtractBackground(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 background substraction

          - a character string specifying the column whose values will
          be used as background 

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

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

