marray: maNorm – R documentation

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maNorm

Simple location and scale normalization function

Description

This function is a simple wrapper function around the main normalization function maNormMain. It allows the user to choose from a set of six basic location and scale normalization procedures. The function operates on an object of class "marrayRaw" (or possibly "marrayNorm", if normalization is performed in several steps) and returns an object of class "marrayNorm".

Usage

maNorm(mbatch, norm=c("printTipLoess", "none", "median", "loess",
"twoD", "scalePrintTipMAD"), subset=TRUE, span=0.4, Mloc=TRUE,
Mscale=TRUE, echo=FALSE, ...)

Arguments

`mbatch`	Object of class `marrayRaw`, containing intensity data for the batch of arrays to be normalized. An object of class `"marrayNorm"` may also be passed if normalization is performed in several steps.
`norm`	Character string specifying the normalization procedures: none no normalization median for global median location normalization loess for global intensity or A-dependent location normalization using the `loess` function twoD for 2D spatial location normalization using the `loess` function printTipLoess for within-print-tip-group intensity dependent location normalization using the `loess` function scalePrintTipMAD for within-print-tip-group intensity dependent location normalization followed by within-print-tip-group scale normalization using the median absolute deviation (MAD). This argument can be specified using the first letter of each method.
`subset`	A "logical" or "numeric" vector indicating the subset of points used to compute the normalization values.
`span`	The argument `span` which controls the degree of smoothing in the `loess` function.
`Mloc`	If `TRUE`, the location normalization values are stored in the slot `maMloc` of the object of class `"marrayNorm"` returned by the function, if `FALSE`, these values are not retained.
`Mscale`	If `TRUE`, the scale normalization values are stored in the slot `maMscale` of the object of class `"marrayNorm"` returned by the function, if `FALSE`, these values are not retained.
`echo`	If `TRUE`, the index of the array currently being normalized is printed.
`...`	Misc arguments

Details

See maNormMain for details and also more general procedures.

Value

mnorm

An object of class "marrayNorm", containing the normalized intensity data.

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.

Examples

# Examples use swirl dataset, for description type ? swirl
data(swirl)

# Global median normalization for swirl arrays 2 and 3
mnorm<-maNorm(swirl[,2:3], norm="median", echo=TRUE)

# Within-print-tip-group loess location normalization for swirl array 1
mnorm<-maNorm(swirl[,1], norm="p", span=0.45)

marray

Exploratory analysis for two-color spotted microarray data

v1.68.0

LGPL

Authors

Yee Hwa (Jean) Yang <jeany@maths.usyd.edu.au> with contributions from Agnes Paquet and Sandrine Dudoit.

Initial release

2009-08-15