Transfer the Illumina data to stabilize the variance

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Description

Transfer the Illumina data to stabilize the variance.

Usage

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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

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.

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.

Author(s)

Pan Du, Simon Lin

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

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## load example data
data(example.lumi)

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

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