maNorm {marray} | R Documentation

## 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.

### See Also

`maNormMain`, `maNormScale`.

### 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)

[Package marray version 1.5.25 Index]