lumi (version 2.24.0)

lumiB: Background correction of Illumina Expression data

Description

Background correction of Illumina Expression data

Usage

lumiB(x.lumi, method = c('none', 'bgAdjust', 'forcePositive', 'bgAdjust.affy'), verbose = TRUE, ...)

Arguments

x.lumi

an ExpressionSet inherited object or a data matrix with columns as samples and rows as genes. For 'bgAdjust' method, it should be a LumiBatch Object

method

the background correction method, it can be any function with a ExpressionSet Object or matrix as the first argument and return an processed object with the same class

verbose

a boolean to decide whether to print out some messages

...

other parameters used by the user provided background correction method

Value

Return an object with background corrected. The class of the return object is the same as the input object x.lumi.

Details

We assume the BeadStudio output data is background corrected. So by default, it will do nothing. The 'bgAdjust' method will estimate the background based on the control probe information, which is kept in the controlData slot of LumiBatch object. The 'forcePositive' method 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. The purpose of this is to avoid NA when do logarithm transformation. 'none' does not but return the LumiBatch object. 'bgAdjust.affy' will call 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.

See Also

bgAdjust, lumiExpresso

Examples

## load example data
data(example.lumi)

## Do the default background correction method
lumi.B <- lumiB(example.lumi, method='bgAdjust', probs=0)