readBeadSummaryData {beadarray} | R Documentation

## Read BeadStudio gene expression output

### Description

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

### Usage

    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, ...)

### Arguments

`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`

### Details

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.

### Value

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

### Author(s)

Mark Dunning and Mike Smith

### See Also

`ExpressionSetIllumina`

### Examples

    ##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)

[Package beadarray version 1.6.0 Index]