AgiMicroRna (version 2.22.0)

tgsNormalization: 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

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)