affyVstRma {lumi} | R Documentation |
Preprocess Affymetrix data by integrating VST with RMA method
affyVstRma(afbatch, bgcorrect.method = "none", bgcorrect.param = list(), VST.param = list(), verbose = TRUE, ...)
afbatch |
a vector of CEL file names or an AffyBatch object, see AffyBatch-class |
bgcorrect.method |
the name of the background adjustment method |
bgcorrect.param |
a list of parameters for bgcorrect.method (if needed/wanted) |
VST.param |
a list of parameters for vst method |
verbose |
logical value. If TRUE it writes out some messages. |
... |
other parameters used by rma function |
This function basically integrates the VST (variance stabilizing transformation) transformation into the rma function in the affy package. The variance stabilization is based on the mean and variance relations of pixel intensities of each probe.
Return an object of class ExpressionSet.
The performance of this function is still under evaluation.
Pan Du