normalizePlateMedian         package:cellHTS         R Documentation

_M_e_d_i_a_n _n_o_r_m_a_l_i_z_a_t_i_o_n _o_f _t_h_e _d_a_t_a _a_n_d _d_a_t_a _t_r_a_n_s_f_o_r_m_a_t_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Plate median normalization of the data 'xraw' of a cellHTS object.
     Optionally, a data transformation such 'log', and a transformation
     to z-scores can be performed.

_U_s_a_g_e:

     normalizePlateMedian(x, transform, zscore)

_A_r_g_u_m_e_n_t_s:

       x: a 'cellHTS' object that has already been configured (see
          details).

transform: a function that takes a numeric vector and returns a numeric
          vector of the same length; for example, the logarithm
          function 'log'.

  zscore: indicates if the data should be centered and scaled after
          normalization and transformation. If missing (default), the
          data will not be centered and scaled. Otherwise, the value of
          this argument should be a character string, either "+" or
          "-", which will be used to set the sign  for the calculated
          z-scores (see details).

_D_e_t_a_i_l_s:

     For each plate, replicate and batch, the median value across the
     wells annotated as 'sample' in 'x$wellAnno' is calculated. Then,
     every measurement is divided by this value.

     If 'transform' is not missing, the chosen data transformation is
     applied.  Most commonly, this option can be used to apply a log
     transformation.

     If 'zscore' is not missing, a robust z-score for each individual
     measurement will be determined for each plate and each well by
     subtracting the overall 'median' and dividing by the overall
     'mad'. These are taken by considering the distribution of
     intensities (over all plates) in the wells whose content is
     annotated as 'sample'.  The allowed values for 'zscore' ("+" or
     "-") are used to set the sign of the calculated z-scores. For
     example, with a 'zscore="-"' a strong decrease in the signal will
     be  represented by a positive z-score, whereas setting
     'zscore="+"',  such a phenotype will be represented by a negative
     z-score.   This option can be set to calculate the results to the
     commonly used convention.

_V_a_l_u_e:

     An object of class 'cellHTS', which is a copy of the argument 'x',
     plus an additional slot 'xnorm' containing the normalized data.
     This is an array of the same dimensions as 'xraw'.

     Moreover, the processing status of the 'cellHTS' object is updated
     in the slot 'state' to 'state["normalized"]=TRUE'.

_A_u_t_h_o_r(_s):

     Ligia Braz ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk

_R_e_f_e_r_e_n_c_e_s:

     ..

_E_x_a_m_p_l_e_s:

      datadir = system.file("KcViabSmall", package = "cellHTS")
      x = readPlateData("Platelist.txt", "KcViabSmall", path=datadir)
      confFile = system.file("KcViabSmall", "Plateconf.txt", package="cellHTS")
      logFile  = system.file("KcViabSmall", "Screenlog.txt", package="cellHTS")
      descripFile  = system.file("KcViabSmall", "DESCRIPTION.txt", package="cellHTS")
      x = configure(x, confFile, logFile, descripFile)
      x = normalizePlateMedian(x, zscore="-")

