lumiExpresso {lumi}R Documentation

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

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.

Value

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

Author(s)

Pan Du

See Also

lumiB, lumiT, lumiN

Examples

## 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'))


[Package lumi version 1.8.3 Index]