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lumi (version 2.24.0)

bgAdjust: Background adjustment for Illumina data

Description

The method adjusts the data by subtracting an offset, which is estimated based on the quantile of the control probes

Usage

bgAdjust(lumiBatch, probs = 0.5, ...)

Arguments

lumiBatch
A LumiBatch object with controlData slot include control probe information
probs
The quantile used to estimate the background
...
other parameters used by quantile method

Value

It returns a LumiBatch object with background adjusted.

Details

The method adjusts the data by subtracting an offset, which is estimated based on the quantile of the control probes. The control probe information is kept in the controlData slot of the LumiBatch object. If no control data information, the method will do nothing.

See Also

lumiB

Examples

Run this code
	data(example.lumi)
	## Here will assume the minimum of the control probe as the background,
	##    because there is no negative control (blank beads) information for the Barnes data.
	example.lumi.b <- bgAdjust(example.lumi, probs=0)

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