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]