normalizeRatio            package:cellHTS            R Documentation

_N_o_r_m_a_l_i_z_a_t_i_o_n _o_f _t_w_o-_c_o_l_o_r _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:

     Normalizes and/or transforms two-channel data 'xraw' of a given
     'cellHTS' object by applying the function defined in 'fun'. The
     default is to take the ratio between the 2 channels (R2/R1). Plate
     median scaling may also be performed.

_U_s_a_g_e:

     normalizeRatio(x, fun=function(r1,r2) r2/r1, log=FALSE, scmedian=FALSE, zscore)

_A_r_g_u_m_e_n_t_s:

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

     fun: a function defined by the user to relate the signal in the
          two color channels 'r1' and 'r2'. 'fun' takes two numeric
          vectors and returns a numeric vector of the same length. The
          default is to take the ration between the two channel.

     log: a logical value indicating whether the result obtained after
          applying  'fun' should be log2 transformed. The default is
          'log = FALSE',  and the data is not log transformed.

scmedian: a logical value indicating whether plate median scaling
          should be performed after applying 'fun' (see details). The
          default is 'scmedian = FALSE'.

  zscore: indicates if the z-scores should be determined after
          normalization and transformation. If missing (default), the
          data will not be scored. Otherwise, it should be a character
          string, either "+" or "-", specifying the sign to use for the
          calculated  z-scores (see details).

_D_e_t_a_i_l_s:

     For each plate and replicate of a two-color experiment, the
     function defined in 'fun' is applied to relate the intensity
     values in the two channels of the 'cellHTS' object. The default is
     to calculate the ration between the second and the first channels,
     but other options can be defined.

     If 'log = TRUE', the data obtained after applying 'fun' is  log2
     transformed. The default is 'log = FALSE'.

     If 'scmedian = TRUE', plate median scaling will be further
     performed, by dividing each measurement by the median value across
     the wells annotated as 'sample' in the respective plate and
     replicate. Note that if the data have been log transformed ('log =
     TRUE'),  the median is subtracted instead. The default is
     'scmedian = FALSE'.

     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.
     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.

_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', except in the
     dimension corresponding to the number of channels, since the
     two-channel intensities have been combined into one intensity
     value.

     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("TwoColorScreen", package = "cellHTS")
     x = readPlateData("Platelist.txt", "TwoColorData", path=datadir)
     confFile = system.file("TwoColorScreen", "Plateconf.txt", package="cellHTS")
     logFile  = system.file("TwoColorScreen", "Screenlog.txt", package="cellHTS")
     descripFile  = system.file("TwoColorScreen", "Description.txt", package="cellHTS")
     x = configure(x, confFile, logFile, descripFile)
     #writeReport(x)
     x = normalizeRatio(x, fun=function(x,y) x/y, log=TRUE, scmedian=TRUE)
     #writeReport(x, force=TRUE, plotPlateArgs=list(xrange=c(-3,3)))

