tgsNormalization {AgiMicroRna} | R Documentation

## Normalization Between Arrays

### Description

Normalization between arrays of the Total Gene Signal. The function is a wrapper of the 'limma' 'normalizeBetweenArrays' with ('none','quantile','scale') methods

### Usage

    tgsNormalization(ddTGS, NORMmethod = "quantile", makePLOTpre = FALSE, makePLOTpost = FALSE, targets,verbose=FALSE)

### Arguments

`ddTGS` | uRNAList, containing the output from `tgsMicroRna`
`NORMmethod` | character specifying the normalization method, 'none','quantile','scale'. The default is `quantile`
`makePLOTpre` | logical, if `TRUE` QC plots with the Raw Total Gene Signal are displayed
`makePLOTpost` | logical, if `TRUE` QC plots with the Normalized Total Gene Signal are displayed
`targets` | data.frame with the target structure
`verbose` | logical, if `TRUE` prints out output

### Value

A uRNAList object containing the Normalized Total Gene Signal in log 2 scale

### Author(s)

Pedro Lopez-Romero

### References

Smyth, G. K. (2005). Limma: linear models for microarray data. In: 'Bioinformatics and Computational Biology Solutions Using R and Bioconductor'. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (eds), Springer, New York, pages 397 - 420

Smyth, G. K., and Speed, T. P. (2003). Normalization of cDNA microarray data. Methods 31, 265-273.

### Examples

    ## Not run:
    data(dd.micro)
    data(targets.micro)
    ddTGS=tgsMicroRna(dd.micro,half=TRUE,makePLOT=FALSE,verbose=FALSE)

    ddNORM=tgsNormalization(ddTGS,'quantile',
                    makePLOTpre=FALSE,makePLOTpost=TRUE,targets.micro,verbose=TRUE)
    graphics.off()

    ## End(Not run)

[Package AgiMicroRna version 2.38.0 Index]