readBeadSummaryData        package:beadarray        R Documentation

_R_e_a_d _B_e_a_d_S_t_u_d_i_o _g_e_n_e _e_x_p_r_e_s_s_i_o_n _o_u_t_p_u_t

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

     Function to read the output of Illumina's software into beadarray

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

     readBeadSummaryData(dataFile, qcFile=NULL, sampleSheet=NULL,
     header=TRUE, sep="\t", ProbeID="TargetID",skip=8,
                                        columns = list(exprs = "AVG_Signal", NoBeads = "Avg_NBEADS",
                                          Detection="Detection", se.exprs="BEAD_STDERR", Narrays="NARRAYS", arrayStDev = "ARRAY_STDEV"),
                                        qc.columns = list(ControlID="TargetID",exprs="AVG_Signal", Detection="Detection", Narrays="NARRAYS", se.exprs="BEAD_STDERR", NoBeads="Avg_NBEADS", arrayStDev="ARRAY_STDEV"), annoPkg=NULL,
                                        qc.sep="\t", qc.skip=8, ...)

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

dataFile: character string specifying the name of the file containing
          BeadStudio output

  qcFile: optional character string giving the location of the control
          probe profile exported from BeadStudio

sampleSheet: optional character string used to specify a sample
          infomation file

     sep: seperator character for the dataFile

  header: set to TRUE if the dataFile contains column headings

    skip: number of header lines to ignore at the top of dataFile

 ProbeID: name of the column heading that contains the probe IDs that
          can be used to uniquely identify each row

 columns: list defining which column headings are to be read from
          dataFile and which slots in the ExpressionSetIllumina object
          they correspond to

qc.columns: list defining which column headings are to be read from the
          qcFile and which items in the QCInfo slot of
          ExpressionSetIllumina they correspond to

 annoPkg: character string specifying the annotation package  name for
          the arrays being read in (only available for certain 
          expression arrays at present)

  qc.sep: seperator character for qcFile

 qc.skip: number of lines to skip at the top of qcFile

     ...: further arguments to be passed to 'read.table'

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

     This function can be used to read gene expression data exported
     from versions 1,2 and 3 of the Illumina BeadStudio application.
     The format of the BeadStudio output may depend on the version
     number. For example, the file may be comma or tab seperated of
     have header information at the top of the file. The parameters sep
     and skip can be used to adapt the function as required. 
     Currently, the default options have been set to handle version 3
     output.

     The format of the BeadStudio file is assumed to have one row for
     each probe sequence in the experiment and a set number of columns
     for each array. The columns for each array are chosen from the
     user within BeadStudio. These can include the average expression
     for each probe, the standard error and the number of beads and
     more.

     With version 2 of BeadStudio it is possible to export annotation
     and sequence information. We recommend this data is not exported
     if the file is to be read into beadarray as it can be retrieved
     later on from other Bioconductor packages.

     It is assumed that the average bead intensities for each array
     appear in columns with headings of the form 'AVG_Signal-ARRAY1',
     'AVG_Signal-ARRAY2',...,'AVG_Signal-ARRAYN' for the N arrays found
     in the file. All other columns headings are found in the same way.

     The default object created by readBeadSummaryData is an
     ExpressionSetIllumina object with enough slots to store all the
     columns that it is possible to export from BeadStudio. The columns
     parameter can be used to select which slots can be found from the
     data and the relevant column headings.

     If quality control information has been exported from BeadStudio
     (control probe profile) this may be read into beadarray too. The
     qc.skip and qc.sep and qc.columns parameters can be used to adjust
     for the contents of the file.

     Sample sheet information can also be used. This is a file format
     used by Illumina to specify the contents of each array in the
     experiment.

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

     An ExpressionSetIllumina object with the slots defined in the
     columns parameter filled with data from the input file.

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

     Mark Dunning and Mike Smith

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

     'ExpressionSetIllumina'

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

     ##code to read the example BeadStudio (version 2) output distributed with the package
     #dataFile = "raw_data.csv"
     #sampleSheet = "raw_data_sample_sheet.csv"
     #qcFile = "raw_data_qcinfo.csv"
     #BSData <- readBeadSummaryData(dataFile, qcFile=qcFile, sampleSheet=sampleSheet,skip=7, columns=list(exprs="AVG_Signal", se.exprs="BEAD_STDEV", NoBeads="Avg_NBEADS"), qc.columns=list(exprs="AVG.Signal", se.exprs="SeqVAR"),qc.sep="," ,sep=",", qc.skip=7)

