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

In MBCB: MBCB (Model-based Background Correction for 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:

NP:

The background corrected values of the Non-Parametric method (or an empty data.frame if this method was not used).

RMA:

The background corrected values of the RMA method (or an empty data.frame if this method was not used).

MLE:

The background corrected values of the MLE method (or an empty data.frame if this method was not used).

Bayes:

The background corrected values of the Bayesian method (or an empty data.frame if this method was not used).

Average Values

AvgNP:

A data.frame of statistics pertaining to the average of the NP normalization method (or an empty data.frame if this method was not used).

AvgRMA:

A data.frame of statistics pertaining to the average of the RMA method (or an empty data.frame if this method was not used).

AvgMLE:

A data.frame of statistics pertaining to the average of the MLE method (or an empty data.frame if this method was not used).

AvgBayes:

A data.frame of statistics pertaining to the average of the Bayesian method (or an empty data.frame if this method was not used).

These values have not been normalized or log2 transformed. See mbcb.main for such functionality.

Author(s)

Yang Xie [e-mail], Min Chen [e-mail], Jeff Allen [e-mail]

See Also

mbcb.main

Examples

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

MBCB documentation built on Nov. 8, 2020, 5:49 p.m.