lumi (version 2.24.0)

lumiT: Transfer the Illumina data to stabilize the variance

Description

Transfer the Illumina data to stabilize the variance.

Usage

lumiT(x.lumi, method = c("vst", 'log2', 'cubicRoot'), ifPlot = FALSE, simpleOutput = TRUE, verbose = TRUE, ...)

Arguments

x.lumi

LumiBatch object

method

four methods are supported: "vst", "log2", "cubicRoot"

ifPlot

determine whether to plot the intermediate results

simpleOutput

determine whether to simplify the output LumiBatch object, which will set the se.exprs, detection and beadNum slots as NULL.

verbose

a boolean to decide whether to print out some messages

...

other parameters used by vst

Value

Return a LumiBatch object with transformed expression values. It also includes the VST transform function and its parameters as attributes: "transformFun", "parameter". See inverseVST for details.

Details

lumiT is an interface of difference variance stabilizing transformation. See vst for details of VST (Variance Stabilizing Transform) of Illumina data.

NOTE: This correction of STDERR as STDEV was moved to the lumiR function.

References

Lin, S.M., Du, P., Kibbe, W.A., (2008) 'Model-based Variance-stabilizing Transformation for Illumina Microarray Data', Nucleic Acids Res. 36, e11

See Also

vst

Examples

## load example data
data(example.lumi)

## Do default VST variance stabilizing transform
lumi.T <- lumiT(example.lumi, ifPlot=TRUE)