MBCB (version 1.26.0)

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

Description

This function is used to background-correct the provided data using the selected correction methods. Normalization is not applied.

Usage

mbcb.correct (g, 
  control, 
  npBool=TRUE, 
  rmaBool=FALSE, 
  mleBool=FALSE, 
  bayesBool=FALSE, 
  gmleBool=FALSE, 
  iter=500, 
  burn=200, 
  isRawBead=FALSE)

Arguments

g

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. Set to true if you wish to compute Non-Parametric background correction.

rmaBool

A boolean value representing the desire to compute the RMA background correction values. Set to true if you wish to compute RMA background correction.

mleBool

A boolean value representing the desire to compute the MLE background correction values. Set to true if you wish to compute MLE background correction.

bayesBool

A boolean value representing the desire to compute the Bayes background correction values. Set to true if you wish to compute Bayes background correction.

gmleBool

A boolean value representing the desire to compute the GMLE background correction values. Set to true if you wish to compute GMLE background correction.

iter

The iteration count; only used in Bayesian correction.

burn

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

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

• This function returns a complex list which can be grouped into two categories: Background-corrected Values: [object Object],[object Object],[object Object],[object Object] Average Values [object Object],[object Object],[object Object],[object Object] These values have not been normalized or log2 transformed. See mbcb.main for such functionality.

See Also

mbcb.main

Examples

data(MBCBExpressionData)
  mbcb.correct(expressionSignal, negativeControl);