Description Usage Arguments Details Value Author(s) References See Also Examples

Wrapper function for two colour microarray data normalization using the P-spline smoother suitable for a RGList- or MarrayRaw-objects.

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`object` |
either a RGList or an MarrayRaw-object. |

`background` |
for background substraction use 'substract'. Default is no backgroud substraction. |

`weights` |
vector of weights that will be used a for a weighted normalization. The default |

`nintervals` |
number of bins in which the data will be divided. The default is 100 bins. |

`showArrays` |
either a integer( > 0) or a vector of integers indicating the arrays for which a MA-plot will be produced. |

`subset` |
subset of the data on which the normalization will be based. A special case of weighted normalization. |

`verbose` |
if |

.

`line.col, line.lty, line.lwd` |
line colour, type and width that will be used in the plots, defaults are col=2, lty=1 and lwd=2. |

`...` |
additional graphical arguments for plotting. |

if necessary?

The value that will be returned is either a MAList or MarrayNorm-object dependening on the input type.

Chantal van Leeuwen and Maarten van Iterson

van Iterson M, Duijkers FA, Meijerink JP, Admiraal P, van Ommen GJ, Boer JM, van Noesel MM, Menezes RX (2012). A novel and fast normalization method for high-density arrays. SAGMB, 11(4).

Paul .H.C. Eilers and Brain D. Marx (1996). Flexible smoothing with B-splines and Penalties. Statistical Science, Vol 11, No. 2, 89-121.

`normalizeWithinArrays, maNormMain`

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