bg.adjust.affinities {gcrma} | R Documentation |

## Background adjustment with sequence information (internal function)

### Description

An internal function to be used by `gcrma`

.

### Usage

bg.adjust.fullmodel(pms,mms,ncs=NULL,apm,amm,anc=NULL,index.affinities,k=k,rho=.7,fast)
bg.adjust.affinities(pms,ncs,apm,anc,index.affinities,k=k,fast)

### Arguments

`pms` |
PM intensities after optical background correction, before
non-specific-binding correction. |

`mms` |
MM intensities after optical background correction, before
non-specific-binding correction. |

`ncs` |
Negative control probe intensities after optical background correction, before
non-specific-binding correction. If `ncs=NULL` , the MM probes
are considered the negative control probes. |

`index.affinities` |
The index of pms with known sequences. (For some types of
arrays the sequences of a small subset of probes are not provided by
Affymetrix.) |

`apm` |
Probe affinities for PM probes with known sequences. |

`amm` |
Probe affinities for MM probes with known sequences. |

`anc` |
Probe affinities for Negative control probes with known
sequences. This is ignored when `ncs=NULL` . |

`rho` |
correlation coefficient of log background intensity in a pair of pm/mm probes. Default=.7 |

`k` |
A tuning parameter. See details |

`fast` |
Logical value. If `TRUE` a faster add-hoc algorithm is
used. |

### Details

Assumes PM=background1+signal,mm=background2,
(log(background1),log(background2))'
follow bivariate normal distribution, signal distribution follows power
law.
`bg.parameters.gcrma`

and `sg.parameters.gcrma`

provide adhoc estimates of the parameters.

the original gcrma uses an emprical bayes estimate. this requiers a
complicated numerical integration. An add-hoc method tries to immitate
the empirical bayes estimate with a PM-B but values of PM-B<`k`

going to `k`

. This can be thought as a shrunken MVUE. For more
details see Wu et al. (2003).

### Value

a vector of same length as x.

### Author(s)

Rafeal Irizarry, Zhijin(Jean) Wu

### See Also

`gcrma`

[Package

*gcrma* version 2.2.0

Index]