marray (version 1.50.0)

maNorm2D: 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

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.

Details

The spot statistic named in z is regressed on spot row and column coordinates, separately within print-tip-group, using the loess function.

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.