Description Usage Arguments Details Value Author(s) Examples

View source: R/normalize.scaling.R

Allows the user to apply scaling normalization.

1 2 3 4 | ```
normalize.scaling(X,trim=0.02, baseline=-1, log.scalefactors=FALSE)
normalize.AffyBatch.scaling(abatch,
type=c("together","pmonly","mmonly","separate"),
trim=0.02, baseline=-1, log.scalefactors=FALSE)
``` |

`X` |
A matrix. The columns of which are to be normalized. |

`abatch` |
An |

`type` |
A parameter controlling how normalization is applied to the Affybatch. |

`trim` |
How much to trim from the top and bottom before computing the mean when using the scaling normalization. |

`baseline` |
Index of array to use as baseline, negative values (-1,-2,-3,-4) control different baseline selection methods. |

`log.scalefactors` |
Compute the scale factors based on log2 transformed data. |

These function carries out scaling normalization of expression values.

A normalized `ExpressionSet`

.

Ben Bolstad, bmb@bmbolstad.com

1 2 3 4 | ```
if (require(affydata)) {
data(Dilution)
normalize.AffyBatch.scaling(Dilution)
}
``` |

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