inverseVST {lumi} | R Documentation |
Inverse transform of VST (variance stabilizing transform), see vst
.
inverseVST(x, fun = c('asinh', 'log'), parameter)
x |
a VST transformed LumiBatch object or a numeric matrix or vector |
fun |
function used in VST transform |
parameter |
parameter of VST function |
Recover the raw data from VST transformed data returned by vst
.
This function can be directly applied to the VST transformed or VST + RSN normalized LumiBatch object to reverse transform the data to the original scale.
Return the raw data before VST transform
Pan Du
Lin, S.M., Du, P., Kibbe, W.A., "Model-based Variance-stabilizing Transformation for Illumina Mi-croarray Data", submitted
## load example data data(example.lumi) ## get the gene expression mean for one chip u <- exprs(example.lumi)[,1] ## get the gene standard deviation for one chip std <- se.exprs(example.lumi)[,1] ## do variance stabilizing transform transformedU <- vst(u, std) ## do inverse transform and recover the raw data parameter <- attr(transformedU, 'parameter') transformFun <- attr(transformedU, 'transformFun') recoveredU <- inverseVST(transformedU, fun=transformFun, parameter=parameter) ## compare with the raw data print(u[1:5]) print(recoveredU[1:5]) ## do inverse transform of the VST + RSN processed data lumi.N <- lumiExpresso(example.lumi[,1:2]) ## Inverse transform. ## Note: as the normalization is involved, the processed data will be different from the raw data. lumi.N.raw <- inverseVST(lumi.N)