Description Details Author(s) References Examples

RMA+ is an extenstion of the RMA algorithm that calculates the probeset intensities of a microarray using a pre-stored RMA model fitted on previously obtained microarrays, e.g. reference microarrays. RMA++ is a further extension based on the RMA+ method. This package depends on the affyPLM package.

Package: | RefPlus |

Type: | Package |

Version: | 1.13.2 |

Date: | 2009-03-11 |

License: | GPL version 2 or newer |

Use `rma.para`

to obtain the reference quantiles and the probe effects from
a reference set, then use `rmaplus`

to calculate the RMA+ intensities based
on the fitted reference quantiles and probe effects.

By Kai-Ming Chang([email protected])

Chang,K.M., Harbron,C., South,M.C. (2006) An Exploration of Extensions to the RMA Algorithm. Available with the RefPlus package.Avaliable with the package.

Harbron, C, Chang, K.M., South,M.C.(2007) RefPlus : an R package extending the RMA Algorithm. Bioinformatics 23, 2493-2494.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
if (require(affydata)) {
## Use Dilution in affydata package
data(Dilution)
##Calculate RMA intensities using the rma function.
Ex0<-exprs(rma(Dilution))
## Background correct, estimate the probe effects, and calculate the
## RMA intensities using rma.para function.
Para<-rma.para(Dilution, bg=TRUE,exp=TRUE)
Ex1<-Para[[3]]
## Calculate the RMA+ intensity using rmaplus function.
Ex2<-rmaplus(Dilution, rmapara=Para, bg = TRUE)
}
``` |

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