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

Run this code

## load example data
data(example.lumi)

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


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