MBCB (version 1.26.0)

mbcb.main: MBCB - Model-Based Background Correction for Illumina Beadarray

Description

This is the main function which incorporates all the others. This should be the most straightforward and autonomous function in the MBCB package.

Usage

mbcb.main (signal,  control,  npBool=TRUE,  rmaBool=FALSE,  mleBool=FALSE,  bayesBool=FALSE,  gmleBool=FALSE,  paramEstFile="param-est",  bgCorrectedFile="bgCorrected",  iter=500,  burn=200,  normMethod="none",  isRawBead=FALSE)

Arguments

signal

The data representing the signal file.

control

The data representing the control file.

npBool

A boolean value representing the desire to compute the non-parametric background correction values.

rmaBool

A boolean value representing the desire to compute the RMA background correction values.

mleBool

A boolean value representing the desire to compute the MLE background correction values.

bayesBool

A boolean value representing the desire to compute the Bayes background correction values.

gmleBool

A boolean value representing the desire to compute the GMLE background correction values.

paramEstFile

The base file name to which suffixes and a file extension will be appended (i.e. 'C:/output'). These files will store the parameter estimates of each background correction method selected.

bgCorrectedFile

The base file name to which suffixes and a file extension will be appended (i.e. 'C:/output'). These files will store the background corrected intensities

iter

The iteration count; only used in Bayesian correction.

burn

The number of iterations which will be burned; only used in Bayesian correction.

normMethod

The normalization method to be used. By default, none will be applied. The choices are: none - no normalization will be applied. quant - Quantile-Quantile normalization will be applied (requires the affy and affyio packages be present). median - Median or Global normalization will be applied.

isRawBead

A boolean value representing whether the input files are bead-level or bead-type. If the input is bead-level, set this value to True so that the raw bead-level values can be summarized to bead-type data.

Value

The function will compute and output log2-tranformed values for the desired background correction methods. Rather than returning this data as R objects, the output is written to files based on the names given in paramEstFile and bgCorrectedFile.

See Also

mbcb.correct mbcb.parseFile

Examples

  data(MBCBExpressionData)
  #Use of global variables is obviously not ideal, but with R's pass-by-value 
  #   setup, we quickly run out of memory without using them on such large 
  #   arrays

  mbcb.main(expressionSignal, negativeControl);