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 1.14.0 Index]