lumiExpresso: From raw Illumina probe intensities to expression values

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

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'))

lumi documentation built on Nov. 8, 2020, 5:27 p.m.