lumiT {lumi}R Documentation

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, stdCorrection = TRUE, simpleOutput = TRUE, ...)

Arguments

x.lumi LumiBatch object
method four methods are supported: "vst", "log2", "cubicRoot"
ifPlot determine whether to plot the intermediate results
stdCorrection determine transfer the standard error of the mean as the standard deviation, used for 'vst' method.
simpleOutput determine whether to simplify the output LumiBatch object, which will set the se.exprs, detection and beadNum slots as NULL.
... 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.

The adding of the parameter "stdCorrection" is for the value correction of the STDEV (or STDERR) columns when 'vst' method is selected. The STDEV (or STDERR) columns of the BeadStudio output file is the standard error of the mean of the bead intensities corresponding to the same probe. (Thanks Gordon Smyth kindly provided this information.). As the variance stabilization (see vst function) requires the information of the standard deviation instead of the standard error of the mean, the value correction is required. The corrected value will be x * sqrt(N), where x is the old value (standard error of the mean), N is the number of beads corresponding to the probe.

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., {it Model-based Variance-stabilizing Transformation for Illumina Microarray Data}, submitted

See Also

vst

Examples


## load example data
data(example.lumi)

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


[Package lumi version 1.4.0 Index]