backgroundCorrectBeads {beadarray} | R Documentation

## Background Correct a BeadLevelList object

### Description

Adapted from 'limma' backgroundCorrect function to correct R intensities of a BLData object using the Rb background values.

### Usage

    backgroundCorrectBeads(BLData, method = "subtract", offset = 0)

### Arguments

`BLData` | BeadLevelList object containing bead level data
`method` | character string specifying correction method. Possible values are '"none"', '"subtract"', '"half"', '"minimum"')
`offset` | numeric value to add to intensities

### Details

If 'method="none"' then the corrected intensities are equal to the foreground intensities, i.e., the background intensities are treated as zero. If 'method="subtract"' then this function simply subtracts the background intensities from the foreground intensities which is the usual background correction method.

The remaining methods are all designed to produce positive corrected intensities. If 'method="half"' then any intensity which is less than 0.5 after background subtraction is reset to be equal to 0.5. If 'method="minimum"' then any intensity which is zero or negative after background subtraction is set equal to half the minimum of the positive corrected intensities for that array.

The 'offset' can be used to add a constant to the intensities before log-transforming, so that the log-ratios are shrunk towards zero at the lower intensities. This may eliminate or reverse the usual 'fanning' of log-ratios at low intensities associated with local background subtraction.

### Value

An 'BeadLevelList' object in which components 'R' and 'G' are background corrected

### Author(s)

Mark Dunning using limma function

### Examples

    data(BLData)

    #default is to simply subtract Rb from R

    BLData.bc = backgroundCorrectBeads(BLData)

    min(BLData.bc$R)

    #Use 'minimum' method to stop negative values

    BLData.min = backgroundCorrectBeads(BLData, method="minimum")

    min(BLData.min$R)

[Package beadarray version 1.0.0 Index]