summarizeReplicates         package:cellHTS         R Documentation

_S_u_m_m_a_r_i_z_e_s _b_e_t_w_e_e_n _n_o_r_m_a_l_i_z_e_d _r_e_p_l_i_c_a_t_e _v_a_l_u_e_s _g_i_v_e_n _i_n _a _c_e_l_l_H_T_S _o_b_j_e_c_t, _o_b_t_a_i_n_i_n_g _a _s_i_n_g_l_e _z-_s_c_o_r_e _f_o_r _e_a_c_h _p_r_o_b_e

_D_e_s_c_r_i_p_t_i_o_n:

     Summarizes the normalized (and possibly already scored) replicate
     values given in a cellHTS object, and calculates a single z-score
     value for each probe.

     Currently this function is implemented only for single-color data.

_U_s_a_g_e:

     summarizeReplicates(x, zscore, summary="min")

_A_r_g_u_m_e_n_t_s:

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

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

 summary: a character string indicating how to summarize between
          replicated measurements.  One of "min" (default), "mean", or
          "min" can be used (see details).

_D_e_t_a_i_l_s:

     Given the normalized values given in the slot 'xnorm' of 'x', a
     single z-score is calculated for each probe.

     The argument 'zscore' indicates the state of the normalized
     replicate measurements: if 'zscore' is missing, it is assumed that
     the replicates have been scored, by calling 'normalizePlateMedian'
      with the argument 'zscore' equal to "-" or "+"; Otherwise,
     'zscore' should be given, so that a robust z-score  is calculated
     for each plate and each well by subtracting the overall median and
     dividing by the overall mad. The overall median and mad 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.

     Finally, a single z-score per probe is calculated by summarizing
     between scored replicates. If 'summary' is 'mean',  the average of
     replicate values is considered; if it is set to 'max', then the
     maximum of replicate intensities is taken, while if its value is
     set to 'min', the minimum is considered, instead (conservative).

_V_a_l_u_e:

     An object of class 'cellHTS', which is a copy of the argument 'x'
     plus the slot 'score', a numeric vector containing the z-factor
     for each well in every plate. The length of this vector is
     therefore equal to the product between the plateSize and the
     number of plates. Moreover, the processing status of the 'cellHTS'
     object is updated in the slot 'state' to 'state["scored"]= TRUE'.

_A_u_t_h_o_r(_s):

     W. Huber huber@ebi.ac.uk, Ligia Braz ligia@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)
      x = summarizeReplicates(x, zscore="-", summary="min")

