lumiT {lumi} | R Documentation |
Transfer the Illumina data to stabilize the variance.
lumiT(x.lumi, method = c("vst", 'log2', 'cubicRoot'), ifPlot = FALSE, simpleOutput = TRUE, verbose = TRUE, ...)
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 |
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.
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.
Pan Du, Simon Lin
Lin, S.M., Du, P., Kibbe, W.A., (2008) 'Model-based Variance-stabilizing Transformation for Illumina Microarray Data', Nucleic Acids Res. 36, e11
## load example data data(example.lumi) ## Do default VST variance stabilizing transform lumi.T <- lumiT(example.lumi, ifPlot=TRUE)