lumiB {lumi} | R Documentation

## Background correction of Illumina data

### Description

Background correction of Illumina data

### Usage

    lumiB(lumiBatch, method = c('forcePositive', 'none', 'bg.adjust'), ...)

### Arguments

`lumiBatch` | a LumiBatch Object, which can be the return of `lumiR`
`method` | the background correction method, it can be any function with a LumiBatch Object as the first argument and return a LumiBatch Object
`...` | other parameters used by the user provided background correction method

### Details

The default background correction method ('forcePositive') will force all expression values to be positive by adding an offset (minus minimum value plus one), it does nothing if all expression values are positive. 'none' does not but return the lumiBatch object. 'bg.adjust' method is based on the `bg.adjust` function in affy package. User can also provide their own function with a LumiBatch Object as the first argument and return a LumiBatch Object with background corrected.

Thanks Kevin Coombes (M.D. Anderson Cancer Center) suggested adding this function.

### Value

return a LumiBatch Object with background corrected.

### Author(s)

Pan Du, Kevin Coombes

### See Also

`lumiExpresso`

### Examples

    ## load example data
    data(example.lumi)

    ## Do the default background correction method
    lumi.B <- lumiB(example.lumi)

[Package lumi version 1.2.0 Index]