maNormMed {marray}R Documentation

Median location normalization function

Description

This function is used for location normalization using the median of intensity log-ratios for a group of spots. The function should be used as an argument to the main normalization function maNormMain.

Usage

maNormMed(x=NULL, y="maM", subset=TRUE)

Arguments

x Name of accessor method for spot statistic used to stratify the data, usually a layout parameter, e.g. maPrintTip or maPlate. If x is not a character, e.g. NULL, the data are not stratified.
y Name of accessor method for spot statistics, usually maM.
subset A "logical" or "numeric" vector indicating the subset of points used to compute the location normalization values.

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 subtracted from the raw log-ratios. It calls the function maMed, 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.

Y. H. Yang, S. Dudoit, P. Luu, and T. P. Speed (2001). Normalization for cDNA microarray data. In M. L. Bittner, Y. Chen, A. N. Dorsel, and E. R. Dougherty (eds), Microarrays: Optical Technologies and Informatics, Vol. 4266 of Proceedings of SPIE.

Y. H. Yang, S. Dudoit, P. Luu, D. M. Lin, V. Peng, J. Ngai, and T. P. Speed (2002). Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research, Vol. 30, No. 4.

See Also

maNormMain, maMed, median.

Examples

# See examples for maNormMain.


[Package marray version 1.8.0 Index]