createBeadSummaryData {beadarray} | R Documentation

## Produce bead averages

### Description

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

### Usage

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

### Arguments

`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.

### Details

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.

### Value

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.

### Author(s)

Mark Dunning and Mike Smith

### See Also

`findBeadStatus`

### Examples

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

[Package beadarray version 1.12.1 Index]