Takes a CodelinkSet or Codelink object and applies normalization to intensity values.

1 2 3 4 5 6 7 8 | ```
## S4 method for signature 'Codelink'
normalize(object, method="quantiles", log.it=TRUE, preserve=FALSE, weights=NULL, loess.method="fast")
## S4 method for signature 'CodelinkSet'
normalize(object, method="quantile", log.it=TRUE, weights=NULL, loess.method="fast")
## S4 method for signature 'CodelinkSet'
codNormalize(object, method="quantile", log.it=TRUE, weights=NULL, loess.method="fast")
``` |

`object` |
an object of class CodelinkSet or Codelink. |

`...` |
further arguments passed to the normalization functions. |

`method` |
method to use in normalization. |

`log.it` |
logical; if data should be log2. |

`preserve` |
logical; if Ri slot should be preserved. |

`weights` |
weights for method CyclicLoess. |

`loess.method` |
loess method to be used, default to 'fast'. |

Currently supported methods include "median", "quantile" and "loess". Normalization functions are borrowed from the limma package.

If a matrix of weights is passed for CyclicLoess normalization, a vector is constructed taking the lowest weight for each probe.

A CodelinkSet or Codelink object with normalized intensity values.

Diego Diez

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Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

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