ZScorePerScreen           package:RNAither           R Documentation

_Z_S_c_o_r_e _n_o_r_m_a_l_i_z_a_t_i_o_n _p_e_r _e_x_p_e_r_i_m_e_n_t

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

     ZScore normalization not per plate, but per experiment (see Value
     and References)

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

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

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

     The ZScore is defined as the quotient of the difference between an
     intensity value and the median of the experiment, and of the
     median absolute deviation.

     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" 

_R_e_f_e_r_e_n_c_e_s:

     N. Malo et al. Statistical practice in high-throughput screening
     data analysis. Nature Biotech, 24(2): 167-175, 2006.

_S_e_e _A_l_s_o:

     'ZScore', 'BScore'

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

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

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

