mbcb.main: MBCB - Model-Based Background Correction for Illumina...
In MBCB: MBCB (Model-based Background Correction for Beadarray)

Description Usage Arguments Value Note Author(s) See Also Examples

View source: R/bg.MBCBNoBead.R

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

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)

`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.

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.

You can use mbcb.parseFile to create the signal and control matrices from the given files.

Yang Xie Yang.Xie@UTSouthwestern.edu, Min Chen min.chen@phd.mccombs.utexas.edu, Jeff Allen Jeffrey.Allen@UTSouthwestern.edu

mbcb.correct mbcb.parseFile

  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);