summarizeReplicates         package:cellHTS2         R Documentation

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

     This function summarizes the replicate values stored in slot
     'assayData' of a 'cellHTS' object  and calculates a single score
     for each probe. Data are stored in slot 'assayData' overridding
     its current content.

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

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

     summarizeReplicates(object, summary ="min")

_A_r_g_u_m_e_n_t_s:

  object: an object of class 'cellHTS' that has already been normalized
          and scored (see details).

 summary: a character string indicating how to summarize between
          replicate measurements.  One of "min" (default), "mean",
          "median", "max", "rms", "closestToZero", or
          "FurthestFromZero" can be used (see details).

_D_e_t_a_i_l_s:

     A single value per probe is calculated by summarizing between
     scored replicates stored in the slot 'assayData' of 'object'. The
     summary is performed as follows:

        *  If 'summary="mean"', the average of replicate values is
           considered; 

        *  If 'summary="median"', the median of replicate values is
           considered; 

        *  If 'summary="max"', the maximum of replicate intensities is
           taken; 

        *  If 'summary="min"', the minimum is considered, instead; 

        *  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 (useful 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 (useful when both sides of the
           distribution of z-score values are of interest).

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

     The 'cellHTS' object with the summarized scored values stored in
     slot 'assayData'. This is an object of class 'assayData'
     corresponding to a single matrix of dimensions Features x 1.
     Moreover, the processing status of the 'cellHTS' object is updated
     in the slot 'state' to 'object@state[["scored"]]= TRUE'.

_A_u_t_h_o_r(_s):

     W. Huber huber@ebi.ac.uk, Ligia Bras ligia@ebi.ac.uk

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

     Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of
     cell-based RNAi screens, _Genome Biology_ *7*, R66.

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

     'normalizePlates', 'summarizeChannels', 'scoreReplicates',
     'imageScreen'.

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

         data(KcViabSmall)
         # normalize
         x <- normalizePlates(KcViabSmall, scale="multiplicative", method="median", varianceAdjust="none")
         # score the replicates
         x <- scoreReplicates(x, sign="-", method="zscore")
         # summarize the replicates (conservative approach: take the minimum value between replicates)
         x <- summarizeReplicates(x, summary="min")

