createBeadSummaryData       package:beadarray       R Documentation

_P_r_o_d_u_c_e _b_e_a_d _a_v_e_r_a_g_e_s

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

     Produce bead averages for each bead type used in an experiment on
     a specified set of strips/arrays.

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

     createBeadSummaryData(BLData, log=FALSE, imagesPerArray = 1,
                    what="G",  probes = NULL, arrays=NULL, 
                    method="illumina", n=3, trim=0.05)

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

  BLData: 'BeadLevelList'

     log: if TRUE then summarise the log2 intensities of each bead

imagesPerArray: Specifies how many images (strips) there are per array.
           Normally 1 for a SAM and 1 or 2 for a BeadChip. The images
          (strips) from the same array will be combined so that each
          column in the output represents a sample 

    what: character string specifying which intensities/values to
          summarise. See 'getArrayData' for a list of possibilities.

  probes: Specify particular probes to summarise. If left NULL then all
          the probes on the first array are used.

  arrays: integer (scalar or vector) specifying the strips/arrays  to
          summarise. If 'NULL', then all strips/arrays are summarised.

  method: chracter string specifying the summarisation method to use.
          Options are '"illumina"', '"mean"', '"median"', '"trim"' and
          '"winsorise"'.

       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.  Used when 
          'method="illumina"'

    trim: fraction of intensities to remove from the bead summary
          calculations when 'method="trim"', or the fraction of
          intensities to set to the 'trim' and 1-'trim' percentile
          intensities when 'method="winsorize"'.  Default value is
          0.05.

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

     To summarise the raw data using the default method used by
     Illumina ('method="illumina"') we first remove outliers for each
     bead type on each array. Outliers are beads which have an
     intensity greater than 3 median absolute deviations (MADs) from
     the bead median intensity on the original (un-logged) scale. The
     'n' argument can be changed to remove beads with intensity 'n'
     MADs above or below the median. With outliers removed, the average
     (mean) intensities of the remaining beads are calculated along
     with the standard error and number of beads.

     Other summarisation options are also available. When
     'method="mean"', the average and standard error of all beads for a
     given bead type is calculated on each array.  This would be 
     appropriate if the scanner has been set up to exclude outlier
     beads   from the bead level .txt or .csv files.

     When 'method="median"', the middle value is returned along with
     the median absolute deviation (rather than standard error) for
     each bead type. When 'method="trim"', the trimmed mean and
     standard error are calculated and for 'method="winsorize"' the
     winsorised mean and standard error are returned.

     By setting the 'log' argument to 'TRUE', we calculate outliers and
     summary values on the log2-scale.  

     If there are any NAs or Inf values, they are ignored.

     Objects which are created separately by 'createBeadSummaryData'
     may be joined using the 'combine' function.

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

     An 'ExpressionSetIllumina' object (or 'NChannelSet' object for
     two-colour data, when 'what="RG"') in which all components are
     matrices with number of rows equal to the number of bead types for
     the experiment and number of columns equal to the number of
     arrays.

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

     Mark Dunning and Mike Smith

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

     'findBeadStatus'

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

     #produce bead summaries for each array
     data(BLData)
     BSData = createBeadSummaryData(BLData, log=TRUE, what="G")
     dim(BSData)

