lumiExpresso: From raw Illumina probe intensities to expression values

Description

Goes from raw Illumina probe intensities to expression values

Usage

lumiExpresso(lumiBatch, bg.correct = TRUE, bgcorrect.param = list(method='bgAdjust'), variance.stabilize = TRUE, 
	varianceStabilize.param = list(), normalize = TRUE, normalize.param = list(), QC.evaluation = TRUE, 
	QC.param = list(), verbose = TRUE)

Arguments

lumiBatch

a LumiBatch object, which can be the return of lumiR

bg.correct

a boolean to decide whether to do background correction or not

bgcorrect.param

a list of parameters of lumiB

variance.stabilize

a boolean to decide whether to do variance stabilization or not

varianceStabilize.param

a list of parameters of lumiT

normalize

a boolean to decide whether to do normalization or not

normalize.param

a list of parameters of lumiN

QC.evaluation

a boolean to decide whether to do quality control estimation before and after preprocessing

QC.param

a list of parameters of lumiQ

verbose

a boolean to decide whether to print out some messages

Value

return a processed LumiBatch object. The operation history can be track in the history slot of the object.

Details

The function is to encapsulate the major functions of Illumina preprocessing. It is organized in a similar way as the expresso function in affy package.

Examples

Run this code

## load example data
data(example.lumi)

## Do all the default preprocessing in one step
lumi.N <- lumiExpresso(example.lumi)

## Do customized preprocessing. No variance stabilizing or log transform, use Quantile normalization.
lumi.N <- lumiExpresso(example.lumi, variance.stabilize=FALSE, normalize.param = list(method='quantile'))

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