smoothQuantileNormalization

dataMatrix

 a vector of reference sample intensity, which matches the dataMatrix 

 data to be adjusted based on the ref and dataMatrix distribution 

adjData

 whether perform the analysis in log2 scale

logMode

 a parameter used by <code><a rd-options="KernSmooth" href="/link/locpoly?package=lumi&version=2.24.0&to=KernSmooth" data-mini-rdoc="KernSmooth::locpoly">locpoly</a></code> 

bandwidth

degree

 whether print the processing sample names 

verbose

other parameters used by <code><a rd-options="KernSmooth" href="/link/locpoly?package=lumi&version=2.24.0&to=KernSmooth" data-mini-rdoc="KernSmooth::locpoly">locpoly</a></code> 


Smooth quantile normalization with a reference sample


methods

The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

Pan Du

lumi

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

smoothQuantileNormalization function

a vector of reference sample intensity, which matches the dataMatrix

data to be adjusted based on the ref and dataMatrix distribution

whether perform the analysis in log2 scale

a parameter used by <code><a href="locpoly" rd-options="KernSmooth">locpoly</a></code>

whether print the processing sample names

other parameters used by <code><a href="locpoly" rd-options="KernSmooth">locpoly</a></code>

Smooth quantile normalization with a reference sample

smoothQuantileNormalization: Smooth quantile normalization

Description

Usage

Arguments

Value

See Also