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, 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

    ## load example data
    data(example.lumi)

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

[Package lumi version 2.38.0 Index]