maNorm2D {marray} | R Documentation |

## 2D spatial location normalization function

### Description

This function is used for 2D spatial location normalization, using the robust local regression function `loess`

. It should be used as an argument to the main normalization function `maNormMain`

.

### Usage

maNorm2D(x="maSpotRow", y="maSpotCol", z="maM", g="maPrintTip", w=NULL,
subset=TRUE, span=0.4, ...)

### Arguments

`x` |
Name of accessor method for spot row coordinates, usually `maSpotRow` . |

`y` |
Name of accessor method for spot column coordinates, usually `maSpotCol` . |

`z` |
Name of accessor method for spot statistics, usually the log-ratio `maM` . |

`g` |
Name of accessor method for print-tip-group indices, usually `maPrintTip` . |

`w` |
An optional numeric vector of weights. |

`subset` |
A "logical" or "numeric" vector indicating the subset of points used to
compute the fits. |

`span` |
The argument `span` which controls the degree of
smoothing in the `loess` function. |

`...` |
Misc arguments |

### Details

The spot statistic named in `z`

is regressed on spot row and column coordinates, separately within print-tip-group, using the `loess`

function.

### Value

A function with bindings for the above arguments. This latter function takes as argument an object of class `"marrayRaw"`

(or possibly `"marrayNorm"`

), and returns a vector of fitted values to be substracted from the raw log-ratios. It calls the function `ma2D`

, which is not specific to microarray objects.

### Author(s)

Sandrine Dudoit, http://www.stat.berkeley.edu/~sandrine.

### References

S. Dudoit and Y. H. Yang. (2002). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. In G. Parmigiani, E. S. Garrett, R. A. Irizarry and S. L. Zeger, editors, *The Analysis of Gene Expression Data: Methods and Software*, Springer, New York.

### See Also

`maNormMain`

, `ma2D`

, `loess`

.

### Examples

# See examples for maNormMain.

[Package

*marray* version 1.8.0

Index]