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, log=FALSE, n=3, outputValid = FALSE, intProbeID = NULL, ignoreList=NULL, probeIndex=NULL, startSearch=1)

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

  BLData: BeadLevelList object containing bead level data

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

   array: numeric value for the array we want to find outliers on

     log: if TRUE the log2 intensities of each bead will be used to
          find outliers. Otherwise un-logged data is used

       n: numeric value defining a cut-off of 'n' median absolute
          deviations from the mean to determine 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

_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 on the set of values.

     The mean and median absolute deviation of all the bead intensities
     are then calculated. Outliers are beads which have intensity more
     than  'n' median absolute deviations from the mean.

     The default setting for the function is the method used by
     Illumina of un-logged intensities and '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 of row indices relating to the BeadLevelList 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):

     Mark Dunning

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

     'findAllOutliers'

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

     data(BLData)

     findBeadStatus(BLData, 2, 1)

     findBeadStatus(BLData, 2, 1, log=TRUE)

     ##Methods may not always agree

     findBeadStatus(BLData, 6140, 1)

     findBeadStatus(BLData, 6140, 1, log=TRUE)

     ##Increasing value of n selects less outliers

     findBeadStatus(BLData, 6140, 1, n=4)

     findBeadStatus(BLData, 6140, 1, log=TRUE, n=4)

