summarizeReplicates         package:cellHTS         R Documentation

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_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",
          "max", "rms", "closestToZero", or "FurthestFromZero" 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 'normalizePlates' 
     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="mean"', the average of
     replicate values is considered; if  'summary="max"', then the
     maximum of replicate intensities is taken; if 'summary="min"', the
     minimum is considered, instead (conservative); if 'summary="rms"',
     the square root of the mean squared value of the replicates (root
     mean square) is taken as a summary function; if
     'summary="closestToZero"', the value closest to zero is taken as a
     summary (ueful when both sides of the distribution of z-score
     values are of interest); if 'summary="furthestFromZero"', the
     value furthest from zero is taken as a summary (ueful when both
     sides of the distribution of z-score values are of interest)

_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

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

     'normalizePlates', 'summarizeChannels'

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

         data(KcViabSmall)
         x <- normalizePlates(KcViabSmall, normalizationMethod="median")
         x <- summarizeReplicates(x, zscore="-", summary="min")

