createBeadSummaryData {beadarray} | R Documentation

## Produce bead averages

### Description

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

### Usage

    createBeadSummaryData(BLData, log=FALSE, n=3,
                   imagesPerArray = 2, probes = NULL)

### Arguments

`BLData` | an BeadLevelList object
`log` | if TRUE then summarise the log2 intensities of each bead
`n` | use n median absolute deviations from the mean as a cut-off for outliers
`imagesPerArray` | Specifies how many images there are per array. Normally 1 for a SAM and 2 for a BeadChip. The images from the same array will be combined so each column in the output represents a sample
`probes` | Specify particular probes to summarise. If left NULL then all the probes on the first array are used.

### Details

Objects which are created seperately by 'createBeadSummaryData' may be joined by using the `cbind` function.

To summarise each bead type we first have to remove the outliers for the bead type on the array. The default method is the method used by Illumina which uses the raw (un-logged) intensities and categorises outliers as being those beads which have intensity more than 3 median absolute deviations from the bead mean intensity. By setting the log parameter we can use the log2 intensities instead of un-logged and by setting the 'n' parameter we choose beads with intensity 'n' mads from the mean.

With outliers removed, we simply take an average of the green (and red, if present) intensities of the remaining beads and create $G and $R matrices. We also store the number of outliers that were detected for each bead type and the standard error of the remaining beads in the `$GNoBeads` and `$GBeadStDev` (and `$RNoBeads` and `$RBeadStDev` for two-colour data) matrices respectively.

### Value

An ExpressionSetIllumina (bead summary) object (or SnpSetIllumina object for two-colour data) in which all components (G,GBeadStDev ....) are matrices with number of rows equal to the number of bead types for the experiment and number of columns equal to the length of the 'arrays' object.

### Author(s)

Mark Dunning and Mike Smith

### See Also

`findBeadStatus`

### Examples

    ##produce bead summaries for the first array in our BLData object
    #data(BLData)
    #BSData = createBeadSummaryData(BLData, log=TRUE)
    #names(BSData)

[Package beadarray version 1.4.0 Index]