findBeadStatus           package:beadarray           R Documentation

_F_i_n_d _O_u_t_l_i_e_r_s

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

     Function finds all beads which are outliers for a given bead type

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

     findBeadStatus(BLData, probes, array = 1, log = FALSE, what = "G", n = 3,
                outputValid = FALSE, intProbeID = NULL, ignoreList = NULL,
                probeIndex = NULL, startSearch = 1)
     getProbeIntensities(BLData, ProbeIDs, array = 1, log = TRUE, what = "G")

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

  BLData: 'BeadLevelList'

  probes: numeric vector for the ProbeIDs of the bead type we want to
          find outliers for

   array: integer specifying which strip/array to use

     log: if TRUE the intensities will be calculated on the  log2
          scale. Otherwise un-logged data is used

    what: character string specifying which intensities to use.
          Possibilities are '"G"', '"Gb"' for single channel data and
          '"G"', '"Gb"', '"R"' and '"Rb"' for two-colour data

       n: numeric value defining a cut-off for the number of  median
          absolute deviations (MADs) from the median to use for
          determining outliers.  The default value is 3.

outputValid: if TRUE the IDs of beads which are not outliers will be
          output

intProbeID: BLData$ProbeID coerced to vector of integers. Never change
          this, for internal use only

ignoreList: list of ProbeIDs to be omitted from the averaging
          procedure. These could be Illumina internal controls which
          are replicated many thousands of times on arrays

probeIndex: parameter for internal use only

startSearch: integer specify where to start searching for a particular
          ProbeID

ProbeIDs: numeric vector for the ProbeIDs of the bead type we want to
          find outliers for

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

     The intensities of each bead with ProbeID 'probe' on the specified
     array are found and if the 'log' parameter is set to TRUE we do a
     log2 transformation of these values.

     The median and MAD for the bead intensities are then calculated. 
     Outliers are beads which have intensity more than 'n' MADs from
     the median.

     The method used by Illumina is to use un-logged intensities with
     'n' = 3.

     Any beads which have intensity NA are also counted as outliers.

     The function returns only the outliers for a bead type unless the
     outputValid parameter is specified.

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

     List of beadIDs dividing the beads of this bead type into two
     categories. 

   valid: valid beads

outliers: beads which are calculated as outliers

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

     Mike Smith and Mark Dunning

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

     'findAllOutliers'

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

     data(BLData)
     findBeadStatus(BLData, 2, 1, outputValid=TRUE)
     findBeadStatus(BLData, 2, 1, log=TRUE, outputValid=TRUE)
     findBeadStatus(BLData, 23, 1, outputValid=TRUE)
     findBeadStatus(BLData, 23, 1, log=TRUE, outputValid=TRUE)

