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

View source: R/bg.MBCBNoBead.R

This function provides the means of using only the MCMC (Bayesian) background correction method for the Illumina platform.

1 | ```
bg.mcmc(iter=500, burn=200)
``` |

`iter` |
The iteration count for the Baysian correction. |

`burn` |
The number of iterations to burn for the Bayesian correction. |

This function returns an array of alpha, mu, and sigma values representing the values computed during the mcmc trial.

This function makes use of two global variables. It will expect `obsbead`

and `obsnc`

are both established prior to calling this function. Obviously, this is not ideal, but R's pass-by-value functionality hindered the ability to pass these matrices as parameters. Using global variables increases performance substantially.

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

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
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
#all of the signals from sample #2
obsbead <<- expressionSignal[,2]
#the negative control values for this sample
obsnc <<- negativeControl[,2]
#compute the alpha, mu, and sigma values
bg.mcmc();
``` |

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